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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.
492. Detecting
disease-marker associations in shrimp
Genetic markers
applied in regression tree prediction models. 2004. Hizer, S. E., T. M. Wright and D. K. Garcia. Animal Genetics
35:50-52.
The
authors of this paper deploy interesting measurement and statistical techniques for finding
genetic markers for disease resistance. The viral
pathogenic system they work with is IHHNV infecting Penaeus
stylirostris.
They use
real-time PCR to measure viral load after an IHHNV challenge test. This
procedure produces a continuous variable, measured on individuals, and thus has much
greater statistical power than the usual percentage mortality, LD50 or
other group tests. The statistical technique is a sort of discriminant
analysis called "classification and regression tree (CART)
modeling".
Eight RAPD markers were used to discriminate between
resistant and susceptible animals and then, in a second experiment which
provided cross-classification, to predict the viral load. The
prediction was very accurate. As the resistant animals came from the selected broodstock of Super
Shrimp Inc., 20 generations removed from their origin in Panama, and the
susceptible controls were recently collected in the Gulf of California,
the cross-validation actually predicted which population the test animals
came from, not disease resistance as a distinguishable
characteristic. Nevertheless the procedures are up-to-date and useful. dgarcia@csusm.edu
491.
Regulation of larval gene expression controls
final body size
Covariation of
larval gene expression and adult body size in natural populations of
Drosophila melanogaster. 2003. Bochdanovits, Z., van der Klis, H. and G. de Jong. Molecular Biology and
Evolution 20:1760-1766.
Much of the genetic variation in the major components
of fitness is caused by regulation of expression of genes which
code for enzymes and other proteins, rather than by variation in the
sequence of the protein-coding region. But
until recently it has been difficult to get an experimental grip on the
connection between this type of genetic variation and its phenotypic
effects. The new expression array technology (Dec 2003 #441) makes it
possible to study the connection, although still not easily.
The
quantitative trait studied here, in Drosophila, is adult body size, which
varies adaptively among natural populations that live under different
temperature regimes. (Adult body size is also important for crustaceans in
aquaculture, which is why this paper is reviewed here). The experimental
design involved analysis of two populations of isofemale lines (lines
descending from a single inseminated female) at two temperatures.
The
authors found that "... larval gene expression correlated highly with
adult weight, explaining 81% of its natural variation. [!] Of the genes that show a correlation of gene expression with adult
weight, most are involved in cell growth or cell maintenance or are
associated with growth pathways." It seems that the expression of the 19 genes may not be independent. There is some evidence that there may
be a cascade in which only 1 - 3 "master genes" control these 19 genes (see Dec 2003
#441 for a similar phenomenon).
For those willing to speculate on
analogies with arthropods grown in aquaculture, it is interesting that 81%
of the variation in Drosophila adult body size is "explained' -- in
the statistical sense -- by
variation in gene expression at the larval stage. Possibly by a few master
genes. One wonders whether there is a phenotypic effect on the
larvae as well (larger size?) which might allow early selection for adult
size (see Sep 2000
#109). z.bochdanovits@bio.uu.nl
490. Major east-west division in the
ancestry of Macrobrachium
Huxley’s line
demarcates extensive genetic divergence between eastern and western forms
of the giant freshwater prawn, Macrobrachium rosenbergii. 2004. de Bruyn, M., J. A. Wilson and P. B. Mather. Molecular
Phylogenetics and Evolution 30:251-257.
Macrobrachium
rosenbergii is a fresh-water crustacean which lives in brackish water
during its earliest developmental stages. The species is farmed in several
parts of the world where they have learned how to cook it properly,
especially Thailand. As a fresh water species one might expect M.
rosenbergii to show strong zoographical disjunctions and this paper on
16S rRNA mitochondrial gene sequence shows that it does.
Alfred
Russel Wallace, the great Victorian naturalist and explorer who conceived
the idea of natural selection about the same time as Charles Darwin,
noticed that the islands of SE Asia could be divided into two groups, a western group inhabited by wildlife
characteristic of Asia and an eastern group inhabited by Australasian wildlife. We now understand
that the imaginary line which Wallace drew between these biogeographic
regions follows the edge of the Asian continental landmass as it was
exposed during the ice-age periods of low sea level. Huxley's Line is a
modification of Wallace's Line, running
through deeper water and grouping most of the Philippine islands with
Malaysia, Eastern
Indonesia and Australia
An
east-west grouping of M. rosenbergii has been noted before in
morphological and allozyme data. This paper on the evolution of ribosomal
gene sequence shows that Huxley's Line separates the Asian and
Australasian populations of M. rosenbergii into two clades, or
monophyletic groups. Despite the potential for larval dispersal during the
salt-water phase these clades of M. rosenbergii have probably evolved
independently since the Miocene period, 5 - 12 million years ago. The
ancestral population (coalescent OTU) may have lived in the Mekong
drainage in SE
Asia. It's nice to see modern
sequencing techniques and coalescent theory backing up the old heroes of
the Darwinian revolution. Also, now we know what grow out comparisons to
try next in practical Macrobrachium aquaculture genetics. m.debruyn@qut.edu.au
489. Low-level
inbreeding depresses oyster growth
The effects of inbreeding on performance traits of
adult Pacific oysters (Crassostrea gigas). 2004. Evans, F., S. Matson, J. Brake and C.
Langdon. Aquaculture 230:89-98.
This
experimental breeding program found that the growth and yield of
two-year-old animals, but not their survival, were significantly depressed
by a rather low level of inbreeding, F = 0.065 (as would be found in
offspring of parents which share one pair of grandparents). An inbreeding
level of F = .2 reduced survival as well. The lower level of inbreeding
can build up quickly in randomly mated captive populations of highly
fecund animals like oysters unless precautions are taken, e.g. pedigree records and appropriate
mating strategies. evanssan@onid.orst.edu
488. Heritability
of aquacultural traits in cod
Genetic variation for juvenile growth and survival in
Atlantic cod (Gadus morhua). 2004. Gjerde, B., B. F. Terjesen, Y. Barr, I. Lein and
I. Thorland. Aquaculture 236:1667-1177.
The
prospects for cod farming are looking better and better, now that
juveniles can be produced reliably through intensive tank culture.
Apparently the limiting factor is mainly the high growout cost. This
commercial problem offers worthwhile targets for genetic improvement for
traits such as growth rate -- if the traits are heritable.
In this study two, separate sets of full-sib families were generated from wild-caught adults
collected from two regions off Norway. The families were reared separately
and weighed 200 days after the eggs had been fertilized. The full-sib
heritability of size was moderate within populations (0.3) and somewhat
higher across populations (0.5) even though the populations were not
statistically different. Variation in survival was not heritable.
"For both traits, the estimate of the effect common to full-sibs
caused by factors other than additive genetics was quite high (varying
from 0.03 to 0.12), indicating environmental effects common to full-sibs
caused by the separate rearing of the families. Improvements in rearing
technology will likely reduce these environmental effects."
The
statistical methods used to dissect the genetic and environmental common
environment effects in this full sib experimental design are
interesting and provide a useful model. The authors conclude that selection for size (growth) is
worth doing. bjarne.gjerde@akvaforsk.nlh.no
487. Trojan
Frankenmedaka
Transgenic male mating advantage provides opportunity
for Trojan gene effect in a fish. 2004. Howard, R. D., J. A. DeWoody and W. M.
Muir. Proceedings National Academy of Science (US) 101:2934-2938.
A
Trojan is an artificial
construct designed to seduce and beguile itself into a fortress and then
deliver a lethal payload. There are Greek Trojans, computer Trojans and
genetic Trojans.
A type of genetic Trojan
of concern to conservation geneticists is a transgenic animal which is especially strong in one
component of fitness, say mating success, but weak in another, say
fertility or survival. The Trojan payload is delivered when transgenic
animals escape into the wild, monopolize matings with wild animals and
produce unfit offspring. Under certain conditions the Trojan transgene
spreading through the population could lead to extinction (Jul 2000 #85,
May 2001 #196, Aug 2002 #342). Fear of Trojans is an obstacle to the use
of transgenics in aquaculture.
This experiment on transgenic medaka
expressing salmon growth hormone gene shows that in a laboratory setting
transgenic males do indeed have a tremendous mating advantage. This is
due to their superior size and bullying capabilities. Their offspring,
however, have viability problems. The balance of effects is modeled and
shown to lead to extinction even though the wild-type (WT) males try
various sneaky tricks to try to nullify the size advantage of the
transgenics. This sneaky behaviour was about 30% successful. "Finally, we model the impact of alternative mating tactics by
WT males on transgene spread. Such tactics may reduce the rate of
transgene spread, but not the outcome." Predation effects are not included in the validation experiment. See Aug 2001 #224. rhoward@bilbo.bio.purdue.edu
486. Trading-off
immigration against local adaptation
Application of the one-migrant-per-generation rule to
conservation and management. 2004. Wang, J. Conservation Biology 18:332-343.
In practical genetic conservation it is important to know how much
migration is required to prevent inbreeding depression while also
permitting an adaptive response to weak local selection. Most
conservationists have learned that one immigrant per generation is
sufficient to prevent serious inbreeding and genetic drift.
Sewall Wright's argument leading to this conclusion depends on a long list
of assumptions about selective neutrality, population sub-substructure,
gene flow et al.
In this mostly analytical paper J. Wang shows
that the one-per-generation rule is actually pretty good even when the
assumptions of Wright's model are considerably violated. However, the rule
applies to one effective migrant, not one physical migrant (Mar
2002 #307). The two migration rates may be very different in real populations, depending
on variation in sex ratio, reproductive success etc.
Wang discusses the
relationship of the effective number of migrants to the actual number of
migrants of a particular age and sex and shows that the physical migrants
do not always have to be more numerous than the effective migrants.
"Rather, translating the elusive Me[effective migration rate] into the manageable M [actual
migration rate] depends on the specific causes (e.g., biased sex ratio, reproductive
skew) that lead to Ne[effective population number] < N ." Real-world cases in which single immigrants have had large effects on
inbreeding and fitness are described in Sep 2001 #235 and May 2003 #400. Wang suggests that
when relevant information
is insufficient we should stick with Mills and Allendorf's
suggestion of between 1 and 10 physical migrant per generation. jinliang.wang@ioz.ac.uk
485. Costly
heavy-metal resistance soon disappears
Rapid loss of genetically based resistance to metals
after the cleanup of a Superfund site. 2003. Levinton, J. S., E. Suatoni, W. Wallace,
R. Junkins, B. Kelaher and B. J. Allen. Proceedings National Academy of
Science (USA) 100:9889-9891.
There
is a location in the Hudson River which, for 25 years, received waste from
a factory making Ni-Cad batteries. An oligochaete (Limnodrilus
hoffmeister) which is ecologically important in the area rapidly evolved
resistance to cadmium and served as an entry-point for Cd into the food
chain. Limnodrilus is a tubifex worm which is a major benthic food
source for higher trophic levels. There appears to be only one gene,
encoding a metal-binding protein, involved in the adaptation. (See Mar 2003 #398 for
a paper on sequence-level responses to toxicity selection.)
Then, in the
mid 1990s, the site was cleaned up. But was there a lasting negative evolutionary consequence of the pollution, in the form of a population which resists
the toxicity of this heavy metal and can transfer it upwards when
opportunity arises again after the next general election in the USA? Apparently we needn't worry
about this. "The cleanup ... resulted in the maintenance of resistant
forms but then there ensued a rapid loss of resistance in 9–18
generations, showing the potential for ecological restoration to rapidly
reduce the potential for trophic transfer of Cd through the
ecosystem."
The authors suggest that the loss of resistance when
selection was relaxed is due to strong trade-offs between resistance and
both growth and general mortality. See Mar 2002 #300 for another example
of the effect of relaxing selection on fitness. levinton@life.bio.sunysb.edu
484. Trout
that tolerate a lot of mercury
Genetic variation of resistance to mercury poisoning in
steelhead (Oncorhynchus mykiss) alevins. 2003. Blanc, J. M., J. D. McIntyre and R. C.
Simon. Heredity 91:255-261.
A
factorial mating design (all males mated with all females) was used for
this challenge test with methylmercuric chloride (CH3HgCl). This type of
design permits a reasonably complete analysis of additive genetic effects,
common environment and maternal effects using traditional analysis of variance
statistical procedures. Heritability of time-to-die in the fry was high
(0.6). Heritability of survival, an all-or-none trait, was 0.3.
Bioaccumulation of mercury in live and dead fry varied widely but the
variation did not show a significant sire effect, i.e. the variation in
bioaccumulation was not demonstrably genetic. From this the authors
conclude "it seems that resistance to poisoning implies a tolerance
to high levels of mercury rather than a limitation of its
accumulation". This is
unfortunate for trout-eaters who might prefer to see trout dying of
mercury rather than evolving ways to pass it on. See #485 above. jmb@st-pee.inra.fr
483. Egg size variation leads to male fitness variation
The early sperm gets the good egg: mating order effects
in free spawners. 2004. Marshall, D. J., P. D. Steinberg and J. P.
Evans. Proceedings of the Royal Society of London (B):1585 - 1589.
This
paper on sea urchins describes a phenomenon which is interesting in itself
and which may be important in other animals which spawn the same way -- by
releasing a batch of eggs into the water where they are fertilized by
sperm released by a number of males. One would think that this is the
closest one could get in the real world to a theoretical, random-mating
gene pool. Not so. There is variation in the size of eggs released at the
same time, and bigger eggs are fertilized first. Bigger eggs produce
bigger and more fit offspring in sea urchins as in many other animals
(salmon, May 2003 #408). The leftover unfertilized eggs are smaller so the
last male into the pool is a rotten egg (sorry) fertilizes
smaller eggs and has inferior offspring.
One of the consequences is that
egg-size variation magnifies the variance of paternal reproductive
success and thus reduces effective population number. Another effect may
be to reduce the heritability of offspring size in the early stages, and
perhaps all the way through development if initial size differences are
magnified by competition (Aug 2002 #343, Feb 2004 #458). Thus experiments
with planned matings cannot be expected to give the same variance
components (or realized selection response) as free-for-all mating in
which the parents are identified afterwards by genetic markers. Variation
in the numerical component of paternal reproductive success has been noted
before in cod (Aug 2003 #423) and red sea bream (Jan 2002 #283), among
other animals, but I believe that paternal variation related to egg size
has not previously been noticed. See Mar 2002 #304 for another instance of
sperm competition. d.marshall@unsw.edu.au
482. Genetic
purification of an endangered population
Pedigree-based assignment tests for reversing coyote (Canis
latrans) introgression into the wild red wolf (Canis rufus) population.
2003. Miller, C. R., J. R. Adams and L. P. Waits. Molecular Ecology
12:3287-3301.
Microsatellites are used
to detect introgression of unwanted coyote genes into a rehabilitated wild
population of red wolves, in Florida. Animals which are identified as
hybrids are either culled or, if they are close to the wolf-coyote
geographical frontier, sterilized. Standard statistical assignment tests
are used in this paper and the more interesting contribution is the way the
reference gene pools are defined.
The pure coyote gene pool is well
sampled and serves as one reference. The genetic composition of the
founding red wolves is also almost completely known, but many generations
have passed since the founding and a lot of genetic drift must have taken
place. So the authors construct hypothetical populations representing the
two pure species and 1/4, 1/2, 3/4 red wolf hybrids. Some pedigree information is available from the early years and
this, plus ordinary Mendelian theory, is used in a sort of gene-drop
simulation to generate pseudo-distributions of gene frequencies for each
of the hypothetical reference populations at various points in their
histories.
Then individual wolves or "wolves" are assigned to
one or more of the hypothetical populations using standard procedures.
Apparently what works best is to use (coyote) private alleles to make
absolute exclusions whenever this is possible, but to use a maximum
likelihood procedure when a suspect animal doesn't have private alleles.
The expected distribution of the private alleles comes from the
simulation.
This technique might have quite a wide applicability in
genetic conservation whenever (a) the genetic composition of a founding
population is well known and (b) there is some pedigree or at least
effective population size information available since the founding.
"These methods may be valuable in cases where reference databases for
small populations have aged substantially, pedigree information is
available or data are generated from historical samples." mill8560@uidaho.edu
481.
Admirable
genetic analysis of disease resistance
Mapping multiple genetic loci associated with
Ceratomyxa shasta resistance in Oncorhynchus mykiss. 2003. Nichols, K. M., J. Bartholomew and G. H. Thorgaard. Diseases of
Aquatic Organisms 56:145-154.
It has been known for
some time that inheritance of resistance to C. shasta in rainbow trout is
polygenic. However, this new study goes far beyond previous ones in the
sophistication of its experimental design and statistical analysis. It
shows (suggestively, not definitively, because of the small sample size)
how genetic mapping and linkage analysis can lead to the identification
and possible selection of genes providing resistance to pathogens.
In summary, the design is based on crossing
clonal lines which differ in their resistance, then using androgenesis to
produce doubled haploids from the F1 hybrids. (Populations of doubled
haploids display all the variation revealed by segregation in the F1 but
are homozygous as individuals. Neat trick. See Mar 2002 #309.) Resistance is analysed as a continuous (time-to-die) and a binary
(alive/dead) trait. Several standard varieties of linkage and association
analysis were used. The
genes found here may be linked (suggestively not definitively, etc) to
previously mapped IPNV-resistance genes and to important-sounding lectin
and immuno-receptor genes. krista.nichols@noaa.gov
480. Breeding
scheme that maximizes allele diversity
A parallel optimization approach for controlling allele
diversity in conservation schemes. 2003. Vales-Alonso, J., J. Fernández, F. J.
González-Castaño and A. Caballero. Mathematical Biosciences 183:161-173.
Here
we have a procedure for maximizing the number of different alleles which
are conserved in a population, as an alternative to maximizing expected
heterozygosity. Allele diversity is known to be a better indictor of
population bottlenecks, and some also argue that it is a better measure of
the genetic resources a population needs for adapting to novel selection
regimes. Most breeding schemes (but not the minimal kinship approach)
focus on conserving heterozygosity. Here
a procedure is developed for finding the particular set of parental
contributions, out of a larger set of available breeders, which maximizes
long-term allelic diversity.
Since the number of possible combinations of
breeders increases exponentially with population size there are severe
practical problems if a systematic, sequential approach is used to select
candidate breeders. Random trial-and-error isn't efficient either and
furthermore tends to locate local rather than global optima. The authors have developed an optimization algorithm which does the
job, i.e. identifies the breeding set which maximizes the retention of
allele diversity.
The procedure is said to be computationally feasible but
requires the use of parallel processors. Implementation times decrease
linearly with the number of processors. This is not yet a procedure for
aquaculture, but should be of interest to serious genetic conservation
units in government and universities. See Aug 2001 #212, Oct 2001 #249,
Nov 2001 #261, Apr 2004 #473. javier@ait.uvigo.es
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