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.
Gene therapy for WSSV infected Penaeus japonicus
Silencing shrimp white
spot syndrome virus (WSSV) genes by siRNA. 2006. Xu, J., F. Han and X.
Zhang. Antiviral Research in press.
Small RNA molecules,
around 20 base pairs long, have recently (1998) been found to be
profoundly important in gene regulation. (See #549, below.) This regulation includes de-activating the genes of invasive
Geneticists are still
recovering from their chagrin at having overlooked this phenomenon
for five decades. The first Nobel prizes began trickling in a week ago.
The process, called "gene silencing" or "RNA
interference", works somewhat like this: (1) Double-stranded RNA (often
originating directly or indirectly from a pathogen) binds to a protein
complex, Dicer, which cleaves it
into fragments. (2) Another protein complex, RISC,
binds these fragments. One of the RNA strands is eliminated but the other
remains bound to the RISC complex and serves as a probe to detect messenger RNA molecules (e.g. from
viral replication). (3) When an mRNA molecule can pair with the RNA
fragment on RISC, it is bound to
the RISC complex, cleaved and
degraded. The gene producing that particular mRNA has been silenced.
Shrimp have this gene
silencing facility, too. "In this investigation, a specific 21bp
short interfering RNA ... targeting a major envelope protein gene (vp28)
of WSSV was used to induce gene silencing in vivo in Penaeus japonicus
shrimp. ... After three injections ...,
the virus was completely eradicated from WSSV-infected shrimp."
See #549, below, for
another fascinating paper on RNA in shrimp. firstname.lastname@example.org
Comparing genetic distances estimated on different kinds of organisms or
A standardized genetic
differentiation measure. 2005. Hedrick, P. W. Evolution 59:1633-1638.
There are many reasons
for wanting to measure the genetic difference between populations. They
include determination of conservation value, reconstructing the history of
migration, selection and drift, and possibly the enforcement of breeders
rights and intellectual property rights in aquaculture.
markers such as microsatellites are used almost universally for such
studies, and the most commonly used measure of differentiation is GST,
defined as the proportion of genetic variation which resides among
populations. A low GST should indicate that populations are genetically similar.
This paper points out
that GST has a serious flaw when applied to microsatellite data because its maximum value
depends on the level of genetic variation within populations as
well as between them. One's intuitive appreciation of "genetic
differentiation" often breaks down with GST because its value can be very small even when subpopulations (or loci, or
species) have completely different suites of alleles. This can happen when
the heterozygosity of the whole ensemble and the average of the
subpopulations both approach unity.
The author proposes to standardize the GST concept,
essentially by dividing it by its maximum possible value given the
observed heterozygosities. The mathematical underpinnings of the prcedure are carefully
developed and explained. "The standardized measure should allow more
appropriate comparisons between loci with different mutation rates, such
as allozyme and microsatellite loci or mtDNA and Y-chromosome genes. …
In addition, the standardized measure allows comparison of levels of
genetic differentiation in different organisms that may have very
different effective population sizes." Both of these situations are relevant in aquaculture and genetic
conservation. See July 2006 #515 for measures of quantitative trait divergence. email@example.com
Selection for temperature-sensitive sex ratios in Nile tilapia?
Effect of rearing
temperatures on the sex ratios of Oreochromis niloticus populations. 2006. Tessema, M., A. Müller-Belecke and G. Hörstgen-Schwark.
This study confirms
earlier reports that treating O. niloticus with high temperature early in
development can bias sex ratios towards phenotypic males (XX "neomales";
see Jan 2002 #282, Oct 2000 #124.) The distinguishing and interesting
feature of the study is that only one of the two source populations, Lake Manzala,
in Egypt, showed this effect. Fish from Lake Rudolph
in Kenya did not.
In the Manzala population
two-thirds of the high-temperature progenies had more than 80% males,
while sex ratios were normal in the Rudolph fish and their hybrids. The
fish were subjected to three temperature regimes, 18 °C for 20 days, 36
°C for 10 days or 38 °C for 10 days starting on day 10 post
The regional differences
in the temperature effect, plus data on the sex distribution of offspring
of neomales and of maternal and paternal half-sibs lead the authors to
conclude that the temperature effect is under genetic control, and is in
"It was concluded that the sensitivity of sex
determination to temperature treatments is under genetic control and
suggests very promising chances for a selection response." Any
procedure which shows promise of enhancing the male:female sex ratio
should be of considerable commercial interest and a breeding program for
that trait would be fun to design. firstname.lastname@example.org
Shrimp immune system specific for WSSV and other viruses
induces sequence-specific antiviral silencing in addition to nonspecific
immunity in a marine shrimp: convergence of RNA interference and innate
immunity in the invertebrate antiviral response? 2005. Robalino, J.,
T. Bartlett, E. Shepard, S. Prior, G. Jaramillo, E. Scura, R. W. Chapman
et al. Journal of Virology 79:13561-13571.
This study suggests that
shrimp (Litopenaeus vannamei) do have a virus-specific immune response,
the nature of which is entirely different from the vertebrate immune
The trigger for the
response is double-stranded RNA (dsRNA), which constitutes the genome of
some viruses and is generated during the replication of many others. Cells
of plants, vertebrates and invertebrates have quite recently been shown to
attack dsRNA molecules not only as part of an anti-viral response but as
part of a universal gene-regulation mechanism which appears be of enormous
significance during development. The numerous modes of attack on dsRNA
involve other RNA molecules, small ones, called sRNA or siRNA (small
interfering RNA) which "silence" genes by preventing their
translation into protein. (See #552, above.)
L. vannamei were
challenged with WSSV in association with intramuscular injection of
synthetic dsRNA. In some experiments the injected dsRNA coded for WSSV
genes, in others the dsRNA was not related to any virus. The response
variable was shrimp survival.
The effect of dsRNA
injection was dramatic. It appears that dsRNA enhances the survival of
shrimp in two ways: it triggers both a non-specific immune response and a
response which is specific to the base sequence of the viral DNA. The
authors "propose a model of antiviral immunity in shrimp by which
viral dsRNA engages not only innate immune pathways but also an RNAi-like
mechanism to induce potent antiviral responses in vivo.
They also say their study
"suggests, for the first time, the possibility of dual stimulation of
innate immunity and antiviral silencing by dsRNA in an invertebrate".
Well, the authors are right about that. See #552, above, for siRNA
treatment of P. japonicus. email@example.com
Clever use of a salmon Frankengene to predict the evolution of prey
Selection on increased
intrinsic growth rates in coho salmon, Oncorhynchus kisutch. 2005.
Sundström, L. F., L. M. and R. H. Devlin. Evolution 59:1560-1569.
Many factors favour rapid
early growth in salmonids: shorter period of vulnerability to small
predators, more effective defense of feeding territories, easier
physiological transition from fresh to salt water. There is
counter-selection too; rapid growth requires more foraging, with its
attendant predation risk, and fish which emerge early from the gravel
invite the concentrated attention of predators. The optimum growth rate in salmonids should depend on the details
of the environmental food and predation regimes as well as population
density. (See #541, below.)
Can we predict what
will happen when the environment changes? This is a classic set-up for
analysis by evolutionary game theory. In formal game theoretic analysis,
we try to predict whether a wild salmon gene (or genotype) can be
displaced by a faster-growing genotype -- especially one that has
escaped from aquacultural operations. This novel experiment uses
transgenic salmon to address questions about the relative fitness, in
nature, of a single, strategy-altering gene.
The experimental fish
contained a transgenic growth hormone gene back-crossed with wild stocks
for several generations, so that they are genetically wild except for the
gene causing rapid growth. (See
Oct 2003 #438, Jul 2000 #81, Feb 2001 #174.)
The control was the population into which the high-growth transgene had
been introgressed. This transgene more than doubles growth rate when fish
are fed to satiation, as they would be in aquaculture. But this
experimental environment mimicked the less benign environment of natural
streams, with varying natural food supplies and predation risk.
Rapid-growth fish emerged
from the gravel two weeks early, and then all sorts of complicated things
happened, depending on food availability and the predation regime.
"The present study
has shown that a major shift in developmental timing can alter critical
early stages affecting survival and can have a significant effect on
fitness. Furthermore, ecological conditions such as food abundance and
predation pressure can strongly influence the potential for
fast-growing variants to survive under natural conditions. The large-scale
removal of many predatory species around the world may augment the
evolution of increased intrinsic growth rates in some taxa."
Remove the predators, fast-growth genes can increase in frequency.
development may have profound implications for aquatic ecosystems
regardless of whether the animals arise from natural mutation, genetic
variation, or release/escape of genetically modified animals from
contained settings". firstname.lastname@example.org
genetic evaluation of tilapia strains
Genetic evaluation of
four strains of Oreochromis shiranus for harvest body weight in a diallel
cross. 2006. Maluwa, A. O. and B. Gjerde. Aquaculture 259:28-37.
The diallel cross, in
which a set of strains is mated in all possible combinations, is a classic
design for estimating the average genetic differences among strains and
the genetic architecture of traits (architecture in the sense of heterosis,
reciprocal effects, genotype-environment interaction and so on).
This is a fine example of the design applied in an aquacultural
context with modern statistical methods (GLM procedure in SAS). The
African tilapia species O. shiranus is of particular interest in Malawi
for aquacultural as well as conservation reasons. "The results show
that for harvest body weight there are substantial additive genetic and
total heterosis differences among pure and crossbred strains of O.
decisions about national aquaculture breeding programs are being made on
the basis of this experiment. email@example.com
Captive breeders can improve a nearly-extinct population
captive breeders to the wild: Harmful or beneficial? 2004. Theodorou,
K. and D. Couvet. Conservation Genetics 5:1-12.
This paper comes to the
sensible conclusion that supplementing a small, rapidly-inbreeding natural
population can be a good thing. It can be good even if the
frequency of deleterious alleles has increased in the captive source
population because of reduced selection.
Genetic load and
extinction risk in the wild population are decreased by supplementation if "(i) the time length of the supplementation program does not
exceed a reasonable time frame, e.g., 20 generations (ii) introduction of
captive individuals is kept at a low level, i.e., one or two individuals
per generation, (iii) the size of the captive population is reasonably
large, e.g., more than 20 individuals".
Note that the benefit is
genetic, owing to delayed approach to homozygosity in the wild population,
rather than a demographic, reduced risk of random, accidental extinction.
The optimal rate of supplementation is too low for a demographic benefit;
the benefits are genetic. See genetic rescue: May 2000 #51, Aug 2002 #341,
May 2003 #400. firstname.lastname@example.org
Inbreeding depression was not purged in New
endangered species management: is New Zealand out of step with the rest of
the world? 2006. Jamieson, I. G., G. P. Wallis and J. V. Briskie.
Conservation Biology 20:38-47.
Inbreeding is a major threat to
the survival of small, isolated populations of many species. Fortunately,
the same population features which allow deleterious recessive genes to be
expressed as inbreeding depression should also allow them to be purged --
selectively removed -- from a population, if the population can avoid
extinction long enough for this to happen. Whether purging actually occurs
in nature is a matter of dispute.
It has been suggested
that in New
purging may have occurred in many terrestrial bird species which have
recently recovered from severe and prolonged bottlenecks. This paper
reports, however, that even though small populations did recover in
terms of their census numbers, "results from recent field studies in New
indicate that, despite the opportunity for purging, inbreeding depression
is evident in many threatened species".
So to the extent that
this situation is analogous with, say, remnant salmon populations, we
should not hope that the problem of inbreeding depression will resolve
itself over time through natural selection (purging).
The paper argues that
"Although inbreeding depression has not prevented some populations
from recovering from severe bottlenecks, the long-term consequences of
inbreeding and small population size—the loss of genetic variation—are
potentially much more insidious." See genetic rescue paper #546,
Salmon QTLs with large effects on growth
QTL for body weight
and condition factor in Atlantic salmon (Salmo salar): comparative
analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus
alpinus). 2005. Reid, D. P., A. Szanto, B. Glebe, R. G. Danzmann and
M. M. Ferguson. Heredity 94:166-172.
This study of three
full-sib families used a total of 91 microsatellite markers. Two
statistically significant QTLs for body weight and four for condition
factor were identified. "The largest QTL effects for BW (AS-8) [linkage group AS-8] and for condition factor (AS-14) accounted for 20.1
and 24.9% of the trait variation, respectively" . [!]
QTLs were found for both traits, some of which occur "on linkage
groups where similar effects have been detected on the homologous regions
in either rainbow trout (Oncorhynchus mykiss) or Arctic charr (Salvelinus
alpinus)". These sound like commercially important QTLs, potentially
relevant to a selection program. See June 2006 #496, Sept 2001 #236 for
other salmonid QTLs found by some of the same authors. email@example.com
breeds to maximize long-term genetic diversity
Using expected allele
number as objective function to design between and within breed
conservation of farm animal biodiversity. 2005. Simianer, H. Journal
of Animal Breeding and Genetics 122:177-187.
It is known that allele
number (the number of distinguishable alleles at a loci) is a sensitive
measure of the rate at which genetic diversity is being lost through
random drift and extinction in small populations. The author of this paper
proposes using the expected number of alleles segregating in the species
after a given time period as an objective function for conservation
The idea embodied in the
objective function (that is, the quantity to be optimized) is not only to
conserve breeds that are different, i.e. which maximize between-breed
genetic diversity, but also breeds which will contribute maximally to
genetic diversity within breeds. The optimal solution of the function
should maximize scope for artificial selection and natural adaptation to
"A formal approach
is presented to predict this quantity [the solution] based on marker information, accounting for
extinction probability of breeds and effective population size within
breeds as the major component of genetic drift. ...the suggested
methodology provides a general and flexible tool to derive the optimum
conservation strategy in various scenarios." See Aug 2006 #524 on
allele diversity, Sept 2006 #536 for another diversity-maximizing scheme
and June 2006 #494 for economic considerations in breed conservation. firstname.lastname@example.org
A useful and convenient population genetics program in Excel
analysis in Excel. Population genetic software for teaching and research. 2006. URL Peakall, R. and P. E. Smouse. Molecular Ecology Notes 6:288-295.
This useful, convenient
and free Excel-based program for analysing marker and other genetic data
has been thoroughly updated. Its many features include a number of
procedures which appear frequently in these postings, including
"estimation of pairwise relatedness among individuals [and]
tools for genetic tagging applications, including location of matching
genotypes and calculation of probabilities of identity".
The program has a good manual and examples.
This is an especially fine Excel add-in for those who don't do
genetic analyses as often as mental hygiene requires and hate re-learning the stand-alone
programs every couple of years. Documentation
and program downloads from http://www.anu.edu.au/BoZo/GenAlEx/ . E-mail email@example.com
Fast growers get tired easily
Evolution of intrinsic
growth rate: metabolic costs drive trade-offs between growth and swimming
performance in Menidia menidia. 2006. Arnott, S. A., Arnott, S. A., and
D. O. Conover. Evolution 60:1269-1278.
want fast-growing fish that don't waste energy, so it is interesting to
see how growth rate and general metabolic rate co-vary. Atlantic
silversides (Menidia menidia) from two locations are known to have
different intrinsic growth rates and different swimming rates as well (see
Dec 2001 #266).
It is shown in this paper that
"the fast-growth genotype had a significantly greater standard
metabolic rate [as
measured by respirometry] than the slow-growth genotype, but a similar maximum sustainable metabolic
rate when swum to near exhaustion".
genotype eats more and therefore uses more energy for digestion and
assimilation, but has a lower scope for activity (capacity for exercise).
The findings support the authors's hypothesis that in nature, growth is
selected to an optimum which is less than the maximum. In nature, animals
have to be able to escape predators and hunt. In aquaculture, the goal of
artificial selection is generally maximal growth unless there are
trade-offs involving disease or fecundity, which in fact rarely turn up in
any definitive way. Predator avoidance is not an issue. See #548, above,
and Sept 2006 #530
on feed conversion efficiency.
So one expects that
artificial selection should usually be able to increase growth above that
which is found in natural populations. firstname.lastname@example.org