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.
The first shrimp anti-viral gene and protein
a novel gene involved in virus resistance of shrimp Penaeus monodon. 2003. Luo, T., X. Zhang, Z. Shao and X. Xu. FEBS
Very often when a farmed
shrimp population is commercially wiped out by WSSV, a few of the animals
survive. One would like to use them in a breed-the-survivors broodstock
improvement program but this can rarely be done, because the survivors are
assumed to be both infected and infective. The alternative approach to
capturing the genetic superiority of survivors -- if indeed they are
genetically superior -- is to breed their relatives. This approach,
usually in the form of between-family selection, often turns out to be either impossible
or ineffectual in practice. However, if resistance genes can be identified
one could select the individuals which carry them without exposing animals to the disease. Thus the search for disease resistance genes,
or markers closely linked to such genes, is an important goal for
aquaculture genetics. The relative inefficiency of marker assisted
selection (MAS) noted in May
2003 #399 is not relevant if there is no practical alternative.
The authors of this paper
examined a survivor from a WSSV infected farm pond in China and, by using
a differential cDNA procedure, identified a gene which produces a lectin-like
anti-microbial polypeptide. (See Jul 2000 #81 and Jan 2002 #282 for other
differential cDNA experiments, and see May 2000 #55, May 2002 #319 and Oct
2002 #349 for more about anti-microbial polypeptides.) The cDNA resembles
a lectin but apparently has no close affinity with anything previously
reported. The gene fragment was cloned and expressed as a recombinant
protein in E. coli.
"[The recombinant protein] displayed a strong antiviral activity in
inhibiting virus-induced cytopathic effect in fish cell in vitro.
Moreover, a native PmAV protein was isolated from shrimp hemolymph by
immuno-affinity chromatography and confirmed by Western blot." The
native protein was in the hemolymph, not attached to the WSSV, and neither
it nor the recombinant protein caused agglutination. From this the authors
infer that however it works, the molecule is not a recognition factor and
does not inhibit attachment of the virus to the cell membrane (or at least
doesn't do so directly). email@example.com
Why YY tilapia supermales don't produce 100% male offspring
Sex ratios in the progeny of
androgenetic and gynogenetic YY male Nile tilapia, Oreochromis niloticus
L. 2004. Ezaz, M. T., J. M. Myers, S. F. Powell, B. J. McAndrew and D. J.
Penman. Aquaculture 232:205-214.
This new paper from the
Stirling group adds considerably to our understanding of the "YY
Supermale" procedure for producing all-male tilapia (Oct 2003 #435,
Mar 2003 #393, Jun 2002 #332). It is no secret that commercial YY breeding
programs do not, in
fact, produce solely male tilapia, although the sex ratio is strongly
biased in that direction. The public-perception risk associated with
hormonal sex reversal makes it worthwhile to find out why YY supermale
technology doesn't work perfectly, and then fix it.
Temperature modifies the
sex ratio (Jan 2002 #282) and it is strongly suspected that there are sex
modifying genes in the genetic background, outside the XX-XY sex
determination system (Oct 2003 #435). The experiments reported here
comprise progeny tests on offspring of YY males produced by androgenesis
and by mitotic gynogenesis. "The factor(s) that cause departures from
the sex ratios predicted by chromosomal sex determination appear to be
autosomal, heritable, polymorphic and able to influence sex ratios in both
directions [too many
females or too many males] . Furthermore, the results suggest that YY and XX lines
could be developed in which such factors had been selected against, for
example, by elimination of families showing departures from monosex
451. AFLP markers better than microsatellites 2003. Campbell, D., P. Duchesne and L. Bernatchez. Molecular Ecology
This case study (on
whitefish) "showed that given a comparable analytical effort in the
laboratory, AFLP were much more efficient than the microsatellite loci in
discriminating the source of an individual among putative populations.
AFLP resulted in higher assignment success at all levels of stringency and
the log-likelihood differences between populations obtained with AFLP for
each individual were much larger than those obtained with microsatellites.
These results indicate that research involving individual-based population
assignment methods should benefit importantly from the use of AFLP
markers, especially in systems characterized by weak population
structuring." See Aug 2003 #417. The point is, AFLPs are easier than
microsatellites to find and score in large numbers, and they are more
reliable than the earlier RAPD markers. The AFLP statistical analyses were
carried out with AFLPOP, Duchesne & Bernatchez's Excel program
available free at http://www.bio.ulaval.ca/contenu-fra/professeurs/Prof-l-bernatchez.html . Microsatellite analyses were
done with Cornuet's GENECLASS. Louis.Bernatchez@bio.ulaval.ca .
Zeroing in on tilapia MHC2003. Cnaani, A., B.-Y. Lee, M. Ron, G. Hulata,
T. D. Kocher and E. Seroussi. Animal Genetics 34:390-391.
Two loci in the Type I
MHC were found to be closely linked to each other, on linkage group 18,
close to a couple of published microsatellite markers. This could be
useful information for marker assisted selection and other studies on
disease resistance in this species. The most recent tilapia linkage map
can be found at http://hcgs.unh.edu.comp . The major histocompatibility
locus is currently a major focus of fish genetics research. See Mar 2003
#398, Oct 2003 #434 and other citations mentioned therein. firstname.lastname@example.org .
Evaluation of computer programs for estimating genetic relatedness
Maximum-likelihood estimation of
Milligan, B. G. Genetics 163:1153-1167.
effectiveness of all the current genetic relatedness estimators is
reviewed here. Microsatellite-based estimators are potentially useful
substitutes for pedigree records during the founding of
conservation and aquacultural populations (Jan 2002 #283, Mar 2002 #303,
Jan 2003 #375, Aug 2003 #425 and #448 below). The maximum-likelihood (ML)
estimator of Thompson (1975; Ann. Hum. Genet. 39: 173–188) was used as a
benchmark. Other relatedness estimators include Ritland (Dec 2000 #142),
Wang (May 2002 #320), Lynch & Ritland, Queller & Goodnight etc.
The Thompson ML turns out
to have a lower standard error but to be more biased. However, steps can
be taken to remove the bias which in any case is not large. "Although
some nonlikelihood estimators exhibit better performance with respect to
specific metrics under some conditions, none approach the high level of
performance exhibited by the likelihood estimator across all conditions
and all metrics of performance." The author does not mention whether
he will give out the C++ program he wrote to calculate the Thompson ML
estimator. See Sept. 2001 #227 for another review of relatedness estimators. email@example.com
448. Microsatellite relatedness estimator used for minimal kinship selection Paralichthys olivaceus. 2004.
Sekino, M., T. Sugaya, M. Hara and N. Taniguchi. Aquaculture 233:163-172.
Minimal kinship breeding
can help conserve genetic diversity in small populations (Nov 2001
#261, Aug 2002 #335). In MK breeding one identifies and selects breeders
that are least related (in the genealogical sense) to the population as a
whole, and thus most likely to be carrying unique genes. The MK procedure
has become popular for managing rare animal populations in zoos, where
loss of genetic diversity is often an acute problem. It was shown several
years ago (Jan 2002 #283) that microsatellite relatedness estimators could
also be used for MK breeding in aquaculture and genetic conservation when
accurate pedigrees are not available.
The authors of this paper
apply the procedure to a population of Japanese flounder. It worked
reasonably well, although apparently not as well as in (Jan 2002 #283),
perhaps because the hard-to-program Ritland estimator and/or maximum
likelihood estimators of genetic relatedness (see #449 above) were not
Diversity is lost when a hatchery is founded
Loss of genetic variation at
microsatellite loci in hatchery produced abalone in Australia (Haliotis
rubra) and South Africa (Haliotis midae). 2004. Evans, B., J. Bartlett, N. Sweijd, P. Cook and N. G. Elliott.
The first hatchery
generations of abalone were missing an estimated 35% - 62% of the
microsatellite alleles present in the wild populations from which they
were founded. However, this
substantial loss of genetic diversity during the founding of the
population did not noticeably decrease overall heterozygosity.
Allele diversity is known to be the best indicator of the genetic
consequences of small population size and biased sampling of founders. The
diversity lost here was comparable to or even greater than that reported in May
2003 #406 during the founding of an Atlantic halibut hatchery broodstock. firstname.lastname@example.org
Evaluation of computer programs for family identification
Methods of parentage analysis in
natural populations. 2003.
Jones, A. G. and W. R. Ardren. Molecular Ecology 12:2511-2523.
This is a useful
comparative evaluation of the current crop of programs for identifying parent-offspring groups on the basis of
microsatellite and other genetic markers. The authors say, "Our goal
is to provide a comprehensive guide to the existing methods of analysis,
with a particular emphasis on those techniques that have been implemented
into readily available computer software packages. Our intent is to direct
scientists interested in parentage analysis to the correct set of
analytical tools for their particular problems." And that is what the
authors do. email@example.com
Inbreeding depression is more serious under natural conditions
Captivity masks inbreeding
effects on male mating success in butterflies. 2003. Joron, M. and P. M.
Brakefield. Nature 424:191-194.
butterflies were inbred to three levels, F = 0, F = 0.25 and F = 0.375. In laboratory cages inbred males had
somewhat lower mating success than outbred males. Although small the
effect was statistically significant, i.e. not mere bad luck. In a
nearly-natural greenhouse environment inbreeding depression was much
larger, a depression of approximately 50% for males inbred to F=0.375. The authors say
that "Our results have important implications for conservation and
for studies of sexual selection because they show that the behaviours
underlying patterns of mating can be profoundly influenced by a history of
inbreeding or by any restraining experimental conditions".
It is not clear whether
the captive environment represented by aquaculture (including fish
stocking programs) should be considered more or less
"constraining" than the natural environment, but my guess is that it is more constraining. Constraints on mating behaviour in
captivity may have negative genetic consequences other than through
inbreeding, e.g. by interfering with MHC-based choice of mates (Aug 2001
#221). See Aug 2003 #422 for
another study of inbreeding depression in the wild, Jun 2000 #71 for the
effect of inbreeding on shrimp, and Apr 2001 #185, May 2001 #193 and Oct
2002 #347 for other inbreeding experiments on this species of butterfly.
See #442 below for inbreeding effects on salmon behaviour. firstname.lastname@example.org
Beauty is heritable, in trout
Big and beautiful? Quantitative
genetic parameters for appearance of large rainbow trout. 2003. Kause, A., O. Ritola, T. Paananen, U.
Eskelinen and E. Mäntysaari. Journal of Fish Biology 62:610-622.
Body condition, body
shape, skin colour and spottiness of Oncorhynchus
mykiss showed reasonably high heritabilities (0.3 - 0.5) in this Finnish
study, which bodes well for aquacultural breeders interested in selecting
for these traits. Furthermore, the correlation between body weight and
condition factor was positive, i.e. no troubling tradeoffs to worry about.
Traits which required subjective evaluation, such as colour,
were scored on a categorical scale by trained observers, then converted to
an underlying continuous scale for genetic analysis. Apparently this
worked: "A fast method was developed to visually evaluate the
appearance of thousands of individuals, even under harsh field
Lower diversity means lower fitness, in general
Correlation between fitness and
genetic diversity. 2003. Reed, D. H. and R. Frankham. Conservation Biology 17:230-237.
This paper reports the
results of a meta-analysis of 34 published studies in which there were
simultaneous estimates of fitness (or a component thereof), population
size and two important measures of genetic variability: heritability of
quantitative traits and/or heterozygosity at neutral marker loci. "The mean weighted correlation between [both] measures
of genetic diversity, at the population level, and population fitness was
0.4323. The correlation was highly significant and explained 19% of the
variation in fitness. "Our study strengthens concerns that the loss
of heterozygosity has a deleterious effect on population fitness and
supports the IUCN designation of genetic diversity as worthy of
Lower genetic diversity means lower aggression
Aggressiveness is associated
with genetic diversity in landlocked salmon (Salmo salar). 2003. Tiira, K., A. Laurila, N. Peuhkuri, J.
Piironen, E. Ranta and C. R. Primmer. Molecular Ecology 12:2399-2407.
It is not unreasonable to
expect that fitness and aggression are positively correlated in natural
populations of salmon. The authors of this paper predicted the genetic
diversity of offspring from microsatellite data collected on the parents. Fry which
were predicted to have high genetic diversity (by several measures) were
more aggressive than those predicted to have low diversity. "Salmon
fry with low estimated genetic diversity were significantly less
aggressive than fry with high estimated genetic diversity. Closer analysis
of the data suggested that this difference was due to differences in more
costly acts of aggression." The mating design used in this experiment
resulted in the fry having low genetic diversity and low aggression also
being significantly more inbred than animals with high diversity &
aggression. Thus, as is so often the case, the question whether
the results are caused by inbreeding depression or some other consequence
of low genetic diversity, or even by kin-recognition, remains to some
degree open. See #445 above for inbreeding effects on male butterfly behaviour. email@example.com
441. A long-term perspective on
Parallel changes in gene
expression after 20,000 generations of evolution in Escherichia coli. 2003. Cooper, T. F., D. E. Rozen and R. E.
Lenski. Proceedings National Academy of Sciences (US) 100:1072-1077.
It has become possible to
observe the expression of many genes simultaneously and watch them switch
on and off during normal development of an organism, or while it attempts to
cope with pathogens or changing environments. Knowledge of the
pattern and sequence of gene expression will increase our basic
understanding of adaptation to life's contingencies and, we hope, will
also eventually assist in the selective improvement of broodstocks
(aquaculture) and identification of evolutionarily significant populations
(conservation). Experiments on gene expression already noted here are Sep 2001
#233, May 2002 #319 and Jan 2003 #377. There will be a lot more of this
kind of work.
The above-cited studies,
on aquacultural species, involved direct sequencing of cDNA one clone at a
is a time consuming procedure. Much
faster analysis of gene expression is possible for a humans and a few
model organisms with a procedure known variously as genome chip, biochip,
DNA chip, DNA microarray, or gene array. (Note that since GeneChip® is a registered trademark genechip shouldn't be used as a generic
term, at least within earshot of Affymetrix Inc.) In
principle it's simple: probes for the coding regions of thousands of
genes are attached to a solid substrate in a rectangular array. When
labeled cDNA or cRNA from a target organism is flooded over the array it
hybridizes to some of the probes. The amount of label at each site in the
array is measured, and from this measurement it is possible to estimate
the activity of the genes which were switched on and working in the
target, even genes with unknown biological functions. Construction of a
DNA microarray is a complex industrial process and the equipment for doing
it is not available off-the-shelf. DNA microarrays are sold commercially,
not the equipment for making them.
The authors of this paper
allowed populations of the bacterium E. coli to evolve for 20,000
generations in a glucose-limited medium, and then used a DNA microarray
carrying probes for every gene in the E. coli genome. Let us think of this as
a long-term experiment in conservation genetics. (If a comparable experiment were to
be done on Atlantic salmon, 20,000 generations would carry it most of the
way through the coming ice age, by which time salmon DNA microarrays
should be available for purchase.)
The intrinsic rate of
population increase, r was higher in both evolved bacterial clones, showing that
adaptive evolution to this classic evolutionary challenge did occur. The
expression patterns of 59 genes changed relative to the ancestral
population -- the same 59 genes in both clones, even though the
clones evolved in isolation from each other. This seems amazing. Could the
evolution of isolated populations really be so consistent and predictable?
Well, yes and no. It
turns out that the expression of many of the 59 genes is controlled by a
small set of regulatory genes. A mutation in one of the regulatory genes
was identified which caused most of the changes in expression in one
population. When transferred into the ancestral population the mutation
changed the expression pattern of the whole regulon, as predicted, and
also increased r, as predicted. But when the mutation was transferred
into the other evolved population it did not have these effects. In the
second population, a different, still unidentified, regulatory mutation
caused the 59 changes in expression.
So different populations, following different evolutionary paths,
converged on the same
functional solution to their environmental problem. Furthermore, after one possible solution to
challenge was found, the alternative solution was blocked or pre-empted.
If the transgenic "evolved hybrid" is actually less fit than its
evolved host -- something the authors do not mention -- we have observed
the evolution of outbreeding depression. firstname.lastname@example.org