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.
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
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 (??). firstname.lastname@example.org
410. Preserving old breeds because they're nice to have
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.
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
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. email@example.com
409. Individuals which are more inbred carry more
California sea lions. 2003. Acevedo-Whitehouse, K., F. Gulland, D.
Greig and W. Amos. Nature 422:35.
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
408. Hatchery salmon eggs more numerous but less fit for
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.
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
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.
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
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. firstname.lastname@example.org
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.
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. email@example.com
406. Instantaneous loss of diversity as aquaculture
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
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." firstname.lastname@example.org
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.
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.
404. A shrimp map dense enough to find growth QTLs
Genetic mapping of the kuruma prawn Penaeus japonicus
using AFLP markers.
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.
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. email@example.com
403. Human risks from evolving Chilean fish-farm
Bacterial resistance to oxytetracycline in Chilean
salmon farming. 2002. Miranda, C. D. and R. Zemelman. Aquaculture 212:31-47.
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." firstname.lastname@example.org
402. Inbreeding increases population extinction in
Inbreeding and extinction: The effect of environmental
stress and lineage. 2002.
Reed, D. H., D. A. Briscoe and R. Frankham. Conservation Genetics
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.
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. email@example.com
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.
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.
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.
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).
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. firstname.lastname@example.org
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.
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.
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
limits are lower. Interestingly, the reverse seems not to happen -- only
very rarely was the advantageous QTL allele lost during phenotypic
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. email@example.com