Hard-to-find Papers
Apr-May 2003
Main Index
January 2003
Feb-Mar 2003
Apr-May 2003
June-Aug 2003
Sept-Oct 2003
Nov-Dec 2003
Jan-Feb 2004
Mar-Apr 2004
May-June 2004
July 2006
June 2006
August 2006
Sept 2006
Oct 2006
Nov 2006
Dec 2006

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.

411.  Are SNPs ("snips") good markers for aquaculture and conservation? 
         Prospects for inferring pairwise relationships with single nucleotide polymorphisms. 2003. Glaubitz, J. C., O. E. Rhodes Jr. and J. A. Dewoody. Molecular Ecology 12:1039-1047. 
         Single nucleotide polymorphisms (SNPs) are genetic markers in which the there is a difference of only one base pair between the two alleles at the locus. Naturally, there are millions of SNPs  in the genomes of most organisms. Micro-array procedures have been developed for automatically scoring hundreds of SNP loci simultaneously at a low cost per sample. So, how do SNP marker loci stack up against the microsatellite loci which are currently preferred for important tasks such as estimating relatedness among animals when pedigree information is not available?
         The authors of this simulation study found that SNPS do rather poorly for a variety of reasons, including the fact that there are only two alleles with very unequal frequencies at most SNP loci. Whereas the reliable identification of full-sib and half-sib groups when both parents are unknown might require 16 microsatellites, about 100 SNPS are required. Reliable detection of higher-order relatedness (cousins) is very, very difficult.  Yet the cost of developing the SNP loci (not the cost of scoring them) is comparable to the cost of developing microsatellites. So the authors conclude that for the foreseeable future SNPs will not be too useful for providing surrogate pedigrees in wild or captive populations, except perhaps populations of mice where sufficient SNP markers are already known.
         However, there probably is a situation in aquaculture where the low cost and automation potential of SNPs can still be realized: assignment of individual offspring to full-sib groups in closed populations where parental matings are known. This is the essential step in pedigree construction in offspring pools, walk-back selection etc. Four or 5 microsatellites are usually sufficient for this purpose so one might guess -- just by extrapolation -- that 20 SNPs could do the job (??). glaubitz@fnr.purdue.edu

410.  Preserving old breeds because they're nice to have around
         Analysis of the cultural value of local livestock breeds: a methodology. 2003. Gandini, G. C. and E. Villa. Journal of Animal Breeding and Genetics 120:1ff.
         This is an interesting paper on an important topic: how one can rank the conservation value of endangered domestic breeds, given that they probably can't all be protected from the approaching  Juggernaut of high-tech genetic uniformity. (The Juggernaut, according to Webster, was an incarnation of the Indian god Vishnu, whose idol, it was formerly supposed, so excited his worshippers when it was hauled along on a large car during religious rites that they threw themselves under the wheels and were crushed).
         The economic utility of specialized breeds, such as adaptation to harsh conditions, should be relatively easy to evaluate. But the authors of this paper propose that more humane values should be used as well. "Local breeds can be considered cultural properties in relation to their role as historical witnesses as they often play a central part in the agriculture tenures and in the social life of rural populations. Local breeds can also be likened to cultural properties because they contribute to the preservation of ancient local traditions.
         "To analyse the historical value of a local breed, a methodology is proposed which is based on a set of parameters including antiquity, role in the agricultural system, farming techniques, role in landscape, gastronomy, folklore and handicrafts and presence in forms of higher artistic expression....  The analysis [nine cattle breeds] shows that consistent differences can be observed in the cultural values of local breeds, both as historical witness and as custodian, today, of local traditions." Rare breeds often taste better too. gustavo.gandini@unimi.it 

409.  Individuals which are more inbred carry more pathogens 
sea lions. 2003. Acevedo-Whitehouse, K., F. Gulland, D. Greig and W. Amos. Nature 422:35.
         This is another study (see Feb 2000 #9) which demonstrates that inbreeding reduces individual fitness in small, wild populations. The estimator of inbreeding used here is a relatedness measure based on microsatellite allele sharing, devised by one of the authors (Proc. R. Soc. Lond. B 268, 2021–2027, 2001). Samples were taken from 371 stranded (sick) animals which were being rehabilitated at theMarine Mammal  Center in California. Sea lions which were sick from physical trauma, including gunshot wounds, turned out to be the least inbred and were considered to be controls. Animals which were sick for other reasons, infections, parasites, carcinoma etc. were more inbred than the controls. Animals suffering from cancer were most inbred.
         "Our results indicate that …  inbreeding could have a significant impact on conservation programmes and the dynamics of wildlife diseases. The most inbred individuals not only cost more to treat and rehabilitate, but they could also act disproportionately as reservoirs of infectious agents when they are subsequently released." The authors mention MHC (major histocompatibility complex) heterozygosity as a likely link between inbreeding and pathogen resistance (see Mar 2003 #398 and papers cited therein). w.amos@zoo.cam.ac.uk  

408.  Hatchery salmon eggs more numerous but less fit for survival 
         Rapid evolution of egg size in captive salmon. 2003. Heath, D. D., J. W. Heath, C. A. Bryden, R. M. Johnson and C. W. Fox. Science 299:1738-1740. 
         Genetic trade-offs between the major components of fitness (reproduction and survival) are to be expected and are often assumed. Indeed, an entire branch of theoretical ecology, life-history theory, is founded on just that assumption. There have been many convincing demonstrations of fitness trade-offs in natural settings, e.g. selection on colour patterns in guppies. This paper on salmon is important because it appears to go to the heart of a current controversy over how best to preserve endangered salmon (or at least make the fish more numerous). The authors show that during the last 17 years there has been a significant decline in the mean size of the eggs produced by a hatchery population of chinook salmon in British Columbia,Canada. Furthermore, fish in rivers that are heavily supplemented with hatchery salmon showed a steady decrease in egg size.
         The authors also show that there are significant phenotypic trade-offs in the hatchery: within any particular year, egg masses which have smaller eggs also have more eggs, and eggs which are relatively small have lower survival to first feeding. (This is a phenotypic correlation which has been noted here before: Jan 2001 #153.) The authors show that selection for survival is relaxed in the hatchery environment but selection for fecundity is maintained. Therefore the survival/fecundity trade-off has shifted and the evolutionary response of the animals has been to make more eggs. 
         The authors do not provide actual evidence that the numbers of eggs per female has increased over the last 17 years while egg size has been decreasing, but presumably it has. The lack of hard data on this point could make one ever-so-slightly uneasy about the conclusion, especially since the heritability of egg size is reported but not the heritability of egg number nor the genetic correlation between these two fitness traits. Nevertheless it does seem likely that the evolutionary (i.e. genetic) trade-off between the two traits over 17 years is the same as the (phenotypic) trade-off between the properties of contemporaneous egg masses.
         The authors' practical conclusion is "These data indicate that unintentional selection resulting in small egg size is potentially a serious concern for the long-term success of salmonid supplementation efforts, but the effect could be minimized through modified breeding practices". The modification would presumably include making family sizes equal in the hatchery, a precaution which ought to reverse the relative importance of selection among families for fecundity and selection within families for survival. dheath@uwindsor.ca  

407.  Mad cow disease in fish? 
         Identification of cDNAs from Japanese pufferfish (Fugu rubripes) and Atlantic salmon (Salmo salar) coding for homologues to tetrapod prion proteins. 2003. Oidtmann, B., D. Simon, N. Holtkamp, H. Hoffmann and M. Baier. FEBS Letters 538:96-100. 
         This paper reports the discovery of fish cDNAs which encode proteins which are homologous to prion proteins found in cattle, sheep, people and other tetrapods. Mad cow disease and similar diseases are thought to be caused by a transmissible mis-folding in this class of proteins. In addition to the sequence similarity the fish proteins have a number of structural similarities to tetrapod prion proteins and are strongly expressed in the brain (of salmon). The authors mention the possibility of farmed fish contracting some form of mad cow disease but discount it for two reasons: (1) the use of contaminated animal processing waste in fish meal has been stopped, and (2) the likelihood of cross-species transfer of prion disease is known to be a function of sequence homology, and the similarity between these fish cDNAs and the homologous sequences in tetrapods is really not all that high. baierm@rki.de  

406.  Instantaneous loss of diversity as aquaculture begins
         Application of DNA markers to the management of Atlantic halibut (Hippoglossus hippoglossus) broodstock. 2003. Jackson, T. R., D. J. Martin-Robichaud and M. E. Reith. Aquaculture 220:245-259. 
         We can add Atlantic halibut to the list of species that suffer a major loss of genetic diversity the moment they are brought into cultivation. Only 36% of the crosses among wild-caught animals which were conducted in three Canadian hatcheries were actually represented in the first offspring generation. Variation in reproductive success in the parental group reduced their effective population number by 50%. The number of unique alleles, as usual the most sensitive indicator of a bottleneck, dropped by 26% between the wild and the captive offspring.
         Although the authors state that this decrease is marginally significant, a randomization test performed on the published data seems to show a highly significant loss of alleles (p<0.00001) both between the wild and the captive offspring and the parents and offspring. "These observations  ... emphasize the necessity for closely monitoring future matings among these fish and suggest the need to introduce additional genetic variation into this group of Atlantic halibut broodstock." michael.reith@nrc.ca  

405.  How to solve the sample-size problem when estimating allelic diversity
         Estimating allelic richness: effects of sample size and bottlenecks. 2002. Leberg, P. L. Molecular Ecology 11:2445-2449.
         Allelic richness (A) is the mean number of alleles per locus. Obviously, A will increase as the number of animals studied increases until the very rarest allele has finally been found. Small samples are likely to include only the more common alleles. This is a problem in many comparative studies because sample size usually varies all over the place. "Although differences in sampling intensity can bias comparisons of allelic richness (A) among populations, investigators often fail to correct estimates of A for differences in sample size.
        "Methods that standardize A on the basis of the size of the smallest number of samples in a comparison are preferable to other approaches. Rarefaction and repeated random sub sampling provide unbiased estimates of A with the greatest precision and thus provide greatest statistical power to detect differences in variation. Less promising approaches, in terms of bias or precision, include single random sub sampling, eliminating very small samples, using sample size as a covariate or extrapolating estimates obtained from small samples to a larger number of individuals." The author mentions that the program FSTAT is convenient for doing rarefaction. http://www.unil.ch/izea/softwares/fstat.html. ). leberg@louisiana.edu  

404.  A shrimp map dense enough to find growth QTLs
         Genetic mapping of the kuruma prawn Penaeus japonicus using AFLP markers.
         The authors are ultimately looking for genes that affect growth (growth QTLs) so they employed a mapping strategy which involved crosses between the extreme high end and the extreme low end of the size distribution in a group of farmed prawns.
         They deployed 54 primer pairs and found 401 usable marker loci, of which about half could be mapped. The average recombination frequency among linked markers (map separation) was about 10%, which is just within the rule-of-thumb limit for finding associations between neutral markers and QTLs. This is good, as is the total high genome coverage achieved in the study. Markers were dense in some regions of the genome (large linkage groups) and more widely separated in others. The authors have identified "potential regions in the P. japonicus genome that have a role in determining growth performance. Two QTL regions have been identified from the male linkage map (Li et al., unpublished)".
         Separate maps were constructed for each sex, and there is evidence that the female may be the heterogametic sex in this species. The authors argue that AFLP marker systems are better than microsatellites for this sort of work in Penaeus although AFLPs have their scoring problems too. yutao.li@csiro.au  

  403.  Human risks from evolving Chilean fish-farm bacteria
         Bacterial resistance to oxytetracycline in Chilean salmon farming. 2002. Miranda, C. D. and R. Zemelman. Aquaculture 212:31-47.
         In Chile oxytetracycline has been used for controlling bacteria in salmon farms intensively, extensively, and for many years. Now a high proportion of oxytetracycline-resistant gram negative bacteria are found in the feed, animal tissue and especially the effluent water of fish farms. Resistant bacteria are proportionately much more abundant in the effluent than in the incoming water. "Therefore, the environment of these farms might play important roles as reservoirs of bacteria carrying genetic determinants for high-level tetracycline resistance, prompting an important risk to public health for workers involved in fish culturing and processing." cdmirand@ucn.cl 

402.  Inbreeding increases population extinction in stressful environments
         Inbreeding and extinction: The effect of environmental stress and lineage. 2002. Reed, D. H., D. A. Briscoe and R. Frankham. Conservation Genetics 3:301-307.
A large number of replicate populations of Drosophila were progressively inbred in laboratory environments where they were chronically stressed with copper sulphate and/or methanol. The population extinction rate was significantly higher under stress, although even in the benign control environment more than 60% of the lines had gone extinct by the time the inbreeding coefficient reached 0.83. (See Oct 2002 #358 and Mar 2002 #300 for papers by some of the same authors which explain in more detail why the fitness of small populations declines even in benign experimental environments.)  In the present work, "Highly significant differences, among lineages, in extinction risk were detected. The results of this study indicate that wild populations are more vulnerable to inbreeding than indicated by extrapolation from captive environments." DHR757f@SMSU.edu  

401.  Origins of shrimp IHHNV disease
         Geographic variations among infectious hypodermal and hematopoietic necrosis virus (IHHNV) isolates and characteristics of their infection. 2003. Tang, K. F. J., B. T. Poulos, J. Wang, R. M. Redman, H.-H. Shih and D. V. Lightner. Diseases of Aquatic Animals 53:91-99.
         This paper mainly consists of a phylogenetic analysis of an approximately 2 kilobase DNA sequence of the IHHN virus, which is an important disease of penaeid shrimp. The analysis supports the conclusion that IHHNV in Hawaii, as well as in the Americas, originated from the Philippines not continental Asia. The IHHNV now in Taiwan, on the other hand, probably came from Thailand. fengjyu@u.arizona.edu  

400.  Rescued by a lone wolf 
        Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. 2003. Vilà, C., A.-K. Sundqvist, Ø. Flagstad, J. Seddon, S. Björnerfeldt, I. Kojola, A. Casulli et al. Proceedings Royal Society London (B) 270:91-97.
         When a population becomes so small that inbreeding is accumulating rapidly and random drift overwhelms selection, the declining fitness of the population may further decrease its size and increase its inbreeding, drawing it into a fatal spiral called the extinction vortex (Jun 2001 #210). One way out of the spiral is to introduce "new blood", i.e. new breeders, to reduce the inbreeding depression and regain some of the lost genetic diversity. If it works this process is called genetic rescue. The problem is, the new breeders may not be genetically well adapted to the local environment and their hybrid descendents (especially F2 and later) may be even less fit than the original population. This phenomenon is called outbreeding depression (Aug 2002 #342, Apr 2001 #179). Genetic rescue has been demonstrated in laboratory experiments, and both inbreeding and outbreeding depression have been observed in nature. Until now there has been no unequivocal observation of naturally occurring genetic rescue in a wild population.
         The authors of this paper present good evidence that the fitness of a remnant population of the Scandinavian gray wolf has been limited by small size and lack of genetic diversity. For decades the population failed to increase despite protection and for several years had only 10 individuals. Inferred pedigrees showed that only one male and female were the effective founders, and both inbreeding and loss of diversity had been  continued for several decades prior to 1991.
         Then the population suddenly started to grow exponentially, to the point where it now includes about 100 individuals. Recent genetic analysis show marked improvements in inbreeding and genetic diversity. Apparently this was due to the arrival of one lone immigrant wolf, a male, around 1991. 68/72 % of the wolves are descended in part from this individual. The authors argue that natural selection (adaptation) as well as release from inbreeding depression is responsible for the increase in population size (increased intrinsic rate of increase = increased fitness).
         The moral  for genetic conservation is quite clear -- if the  wolf example can be generalized. The occasional natural immigration of spawners from another stream may not be a bad thing for a small salmonid populations. Deliberate genetic rescue of an endangered populations may be a lesser evil than leaving them in an extinction vortex. carles.vila@ebc.uu.se

399.  Phenotypic selection is better than marker assisted or QTL selection 
         Marker assisted selection with optimized contributions of the candidates to selection. 2002. Villanueva, B., R. Pong-Wong and J. A. Woolliams. Genetics Selection Evolution 34:679-703.
         This paper describes a particularly realistic simulation of three types of selection: phenotypic selection in which no genotype information is used, QTL selection in which there is direct selection on an effective gene and marker assisted selection (MAS) in which there is direct selection on a locus which is linked to the effective gene. All the simulations used BLUP and pedigree information to select animals on the basis of their estimated breeding values (EBV), that is, selection was always more sophisticated than simple "breed the biggest".
         Two levels of sophistication were simulated: truncation selection in which the number of parents and family sizes are the same each generation and optimized selection in which these variables are adjusted to maximize genetic gain within a constrained rate of inbreeding (See Apr 2001 #177). Truncation selection is the easiest to perform in practice, especially in aquaculture where record-keeping and on-the-fly breeding choices can be problematic. However, it has been shown that the gains from optimized selection are around 20% higher. The large benefit which can be achieved through optimized selection was shown here too.
         What is noteworthy is that phenotypic selection always gave better long term results than either MAS or QTL selection. What happens is that the emphasis on selecting for one particular gene allows the other additive "background" genes to drop out of the population by chance (inbreeding rate will usually be an indicator of this effect). Thus there is a loss of additive genetic variance with QTL and MAS selection relative to phenotypic selection,  and the ultimate selection limits are lower. Interestingly, the reverse seems not to happen -- only very rarely was the advantageous QTL allele lost during phenotypic selection.
         In the short term both QTL and MAS gave a more rapid initial response than phenotypic selection.  Salmon and some other aquacultural species have such long generation intervals that rapid response could actually be worth more, by an economic calculation like net present value, than a high selection plateau which might not be approached for 100 years.
         In aquaculture there is another situation which is not comparable to these simulations and where MAS and/or QTL selection is likely to be very useful: selection for resistance to specific pathogens. Here we can hope for large QTL effects in a situation where the genetic information inferred from conventional disease challenge tests is usually zero or positively misleading. b.villanueva@ed.sac.ac.uk