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.
Projected tilapia and carp invasion of the Americas
Invasive potential of
common carp (Cyprinus carpio) and Nile tilapia (Oreochromis niloticus) in
American freshwater systems. 2006. Zambrano, L., E. Martínez-Meyer,
N. Menezes and A. T. Peterson. Canadian Journal of Fisheries and Aquatic
A Geographic Information
System (GIS) approach is used to predict the potential -- or inevitable --
distribution of common carp and O. niloticus in the Americas. Ecological
and environmental information from the native distributions of these
species in Asia and Africa is used as "training data" for the
computer program, which then proceeds to identify candidate locations in
the Americas where there appears to be niche space available (by the
Hutchinsonian definition of niche).
Tilapia should be able to
invade the southeastern United States and the coastal lowlands of Mexico
and Central America. In South America the possible range of O. niloticus
includes much of Brazil, Argentina, Venezuela and Guyana. The predicted
carp distributions are more to the north and south in the lowlands, and at
higher elevations in the tropics.
Of course these areas are
not currently free of fish; the invaders muscle into a niche through
successful competition and predation directed at the locals. email@example.com
Does competition among individuals change their breeding values?
of competitive effects in forest tree or animal breeding programs.
2005. Muir, W. M. Genetics 170:1247-1259.
Competition strongly affects growth rate in fish. Competition may in
fact be the most important source of size variation among individuals in a
community tank. Tilapia and carp are notoriously prone to stunting their
growth in the presence of larger fish.
Stunting often involves a
behavioural (or endocrinological) feedback loop which magnifies initial
size variation even when plenty of food is available to everyone. See Dec
2000 #148, Oct 2003 #427, Feb 2004 #456. At the genetic level, a gene
which has a direct positive effect on the growth of an individual will
have a negative effect on the growth of others in the group. All of this
is ignored in standard genetic models of covariation, which may explain
why the results of BLUP-based index selection for growth have often been
disappointing in aquaculture, often conspicuously so.
paper develops a model in which "mixed-model methodology (BLUP) is
utilized to separate effects on the phenotype due to the individuals' own
genes (direct effects) and those from competing individuals (associative
effects) and thereby to allow an optimum index selection on those
effects". The model was tried out in a selection experiment on an
ill-tempered and cannibalistic population of quail.
using standard BLUP selection made no progress but selection on the index
including competitive effects worked much better. "The differences in
response show that competitive effects can be included in breeding
programs, without measuring new traits, so that costs of the breeding
program need not increase."
details of the model are well explained both mathematically and
intuitively. The author plainly wants to be helpful and, in an appendix,
provides SAS code for solving one of the examples in the paper. firstname.lastname@example.org . (Also see another paper which provides BLUPF90 script for applying the same
model to larger problems: J. Anim. Sci. 2005. 83:1241-1246; email@example.com.) firstname.lastname@example.org
Where did Vietnamese WSSV come from?
epidemiology of white spot syndrome virus within Vietnam. 2004. Dieu,
B. T., H. Marks, J. J. Siebenga, R. W. Goldbach, D. Zuidema, T. P. Duong
and J. M. Vlak. Journal of General Virology 85:3607-3618.
WSSV virus shows relatively little variation, either in its genome or its
protein make-up, which suggests that it has emerged recently or recently
experienced a severe bottleneck. RFLP markers are used in this paper to
develop a hypothesis for the biogeography of the spread of WSSV through
Vietnam. The authors propose that WSSV entered Vietnam by multiple
introductions from a common ancestor on one side or the other of the
Taiwan Strait. From there, it probably spread outwards to Thailand, North
Vietnam, China (Hainan) and Cambodia, mutating slightly as it went. See
Aug 2001 #222. email@example.com
Marine protected areas are good for genetic diversity as well as for
of fishing protection on the genetic structure of fish populations.
2006. Pérez-Ruzafa, Á., M. González-Wangüemert, P. Lenfant, C. Marcos
and J. A. García-Charton. Biological Conservation 129:244-255.
protected areas (MPA) are proposed or already established in many parts of
the world, but while their usefulness for conservation at the population
level has been demonstrated, we don't know much about their value at the
"This paper analyses
the effects of fishery protection on the structure of populations of
Diplodus sargus [White sea bream],
a target species, in protected and non-protected areas of the western
Mediterranean. ... Protected areas have significantly higher allelic
richness. The lower levels of heterozygosis and higher heterozygote
deficit showed by islands compared with coastal areas makes clear the
importance of considering the connectivity processes when designing a [MPA]."
Allelic richness was the most statistically significant measure of
the effectiveness of reserves, as might be expected because of its known
sensitivity to genetic drift (See Aug 2006 #524, Oct 2006 #543 for other
papers on allele richness in conservation.) The authors emphasize that
because a lot of the genetic diversity is found between populations,
"the design of marine protected areas must take into account the
spatial heterogeneity in the genetic structure of populations and the
connectivity between protected and non-protected populations as well as
between MPA network constituents".
In other words, a marine
protected area which maintains a population at a viable level will not
necessarily retain or even capture all the relevant genetic diversity. firstname.lastname@example.org
Identification of wild trout families for optimal conservation
within samples of brown trout (Salmo trutta) and implications for
supportive breeding. 2005. Hansen, M. M. and L. F. Jensen.
Conservation Genetics 6:297-305.
natural populations of trout must, by definition, consist of a limited
number of families. But what does "limited" mean in terms of our
technical ability to detect family groups? Can we actually find them with
commonly available technology?
In this study, brown trout resident in two small Danish rivers were
compared with a large anadromous trout population and with simulated
control populations. Microsatellite markers at 8 loci did reveal the
family structure of the resident trout samples; the program SPAGEDI found
meaningful pairwise similarities and the program COLONY (Wang) found
groups of full-sibs nested within half-sibs. "The expected increase of inbreeding coefficient in the two [small river] samples due to family structure was 0.026 and 0.030
respectively." This is
indeed meaningful information in the context of supportive breeding, where
it is advantageous to avoid mating within sibs and to capture as much
family diversity as possible in the founder generation (Jan 2002 #283).
See also Feb 2004 #464 for trout metapopulations and #556, below, for
schooling sibs. email@example.com
Salmon maturation depends more on growth rate than body size
size matter most? The effect of growth history on probabilistic reaction
norm for salmon maturation. 2006. Morita, K. and M. Fukuwaka.
or "precocious" maturation is a serious problem for aquaculture,
and an important component of the reproductive strategy of wild salmon. It
is under strong genetic control, shows marked local adaptation in the
wild, and is environmentally manipulated in aquaculture through the use of
lights and special feeding regimes. Something similar happens with tilapia
under crowded conditions. No one knows for sure exactly how it works in
Reaction norm is a
convenient technical phrase denoting the distribution of phenotypes
expressed by a particular genotype (or strain, or population) under a
variety of environmental conditions. The reaction norm describes the
outcome of a genotype's interaction with its environment; for example,
variation in the light regime. Early maturation in an aquacultural
broodstock can thus be described in terms of the reaction norms of the
available genotypes in the available environments.
salmon, it is known that one environmental factor is body weight, often
recorded as the weight at which 50% of the animals are mature. However,
there are an infinite number of growth trajectories different animals can
follow to reach -- eventually -- a given body weight. So growth
trajectories are also the outcomes of genotypes interacting with
to understand the evolution of the maturation schedule, it is necessary to
comprehend the relationships among body size, growth history, and
maturation schedule." Thorpe, Bromage and many others have been
making this point for decades.
authors of this paper have found something interesting. "Previous growth
history was found to be more closely linked to maturation probability than
body size. The most recent growth condition was the most important factor
affecting whether a fish matured during the subsequent breeding
season." See Sept 2006 #530.
Growth rings on scales were used to
infer growth, size and maturation status. (This also works with tilapia
scales, by the way.) Logistic regression with "mature/immature"
as the response variable was used to gauge the relative importance of body
size vs. annual growth increment. The latter was much more important, in
Note that while this is
not a genetic paper per se it provides a good measurement tool for
genetic comparison of strains or for selection within strains. firstname.lastname@example.org
How antimicrobial diversity is generated in Litopenaeus vannamei
structure and transcriptional regulation of the penaeidin gene family from
Litopenaeus vannamei. 2006. O'Leary, N. A. and P. S. Gross. Gene
produce peptides called penaeidins which are effective
antimicrobial and antifungal agents (see Dec 2003 #453 and references
therein). Like the peptide receptors of the vertebrate MHC immune system,
penaeidins are highly diverse both within and between individual shrimp. This
study helps explain how the genetic diversity of penaeidins is generated.
There are three classes
of penaeidins which are coded by different genes. The genes are so
different that the variety of peptide products is unlikely to result from
alternative splicing of RNA messengers. There appears to be no
post-transcriptional cutting-and-splicing as in the vertebrate MHC.
Instead, "genomic DNA sequence analysis indicates that each penaeidin
class is encoded by its own unique gene with full independent coding
potential, indicating that post-transcriptional mechanisms are not
responsible for ... diversity. Rather, genomic content [i.e.
DNA nucleotide variation in the peptide coding region of the genes]
accounts for all expressed penaeidin classes and isoforms found in
multiple individual shrimp."
real-time PCR was used to demonstrate that the penaeidin genes are
expressed at dramatically different levels". The authors conclude
that there must be variation in the regulatory portions of the genes as
well. See Oct 2006 #549. email@example.com
Can we estimate breeding values of non-identified animals grown
breeding values and accuracies from group in comparison to individual
observations. 2006. Olson, K. M., D. J. Garrick and R. M. Enns.
Journal of Animal Science 84:88-92.
A lot of useful
aquacultural information is measured on groups of animals, not
individuals. Examples are feed intake or food conversion ratio in a tank,
percent survival in a challenge test, fry production from a batch of
It is often easy to
arrange matters so that each tank contains a known set of families. Is
quantitative genetic analysis of pooled data possible, e.g. when every
individual in the tank is assigned the same average value? How accurate
are estimates of breeding value derived from pooled data?
This theoretical and
simulation study of certain analytical designs (sire model, maternal
grandsire model) shows that the loss of accuracy with pooled data in not
as serious as one might expect, especially when the number of individuals
in each tank is small. Furthermore,
designs in which each tank contains animals from only one (sire) family
are not especially sensitive to tank effects, even when the effects cannot
be estimated. (Tank effects can be estimated if every family occupies more
than one tank and every tank contains more than one family.)
It seems, then, that
collecting aquacultural data on pooled individuals might be considered as
a possibly cost-effective tradeoff between genetic accuracy (= more rapid
progress) and the overall expense of a breeding program. The paper (which
is actually about cows, by the way) clearly explains the simple
adjustments to the mixed model which are needed to handle pooled data.
Surprisingly, the intuitive approach which simply assigns each individual
in a pool the same (average) value doesn't work too badly. Competition is
not included in this model (#563, above). firstname.lastname@example.org
schools exhibit population and kin associations beyond juvenile stages. 2005. Fraser, D. J., P. Duchesne and L. Bernatchez. Molecular Ecology
authors sampled individuals from a large number of schools of brook charr (or brook trout; Salvelinus fontinalis) from two
populations and, using microsatellite markers, determined that the number
of siblings found in a school was greater than expected based on assumed
random mixing within the population.
In other words, charr
siblings tend to be found in the same school, just like people siblings.
And for similar reasons: "We discuss the hypothesis that the stable
kin groups, rather than arising from kin selection, may instead be a
by-product of familiarity based on individual selection for the
maintenance of local adaptations related to migration (natal and feeding
"Our results are
noteworthy because they suggest that there is some degree of permanence in
the composition of wild fish schools. Additionally, they support the
hypothesis that schools can be hierarchically structured (from population
members down to family groups) and are thus nonrandom genetic
entities." See #560, above. email@example.com
Tilapia: a better procedure for comparing growth rates of different
response of Nile tilapia fry to salinity stress in the presence of an
'internal reference' fish. 2005. Basiao, Z. U., R. V. Eguia and R. W.
Doyle. Aquaculture Research 36:712-720.
Comparing the growth
rates of different strains can be difficult in aquaculture, especially
when facilities for replication are limited. The problem can be alleviated
by rearing the strains together in the same tank, but then you have the
problem of telling them apart -- by the time they are big enough to tag
they may already have developed different sizes or growth rates for
environmental reasons. Molecular markers can solve this problem but are
An alternative approach
is to use a visually-distinguishable third strain as a standard reference,
or "common denominator" in a series of pairwise tests. (See for
example Feb 2002 #294.) Each of the two test strains is grown from birth
in the presence of reference fish, and by comparing the test strains to
the common reference they can be compared to each other.
A statistical power
analysis conducted on this experiment in the Philippines with three
strains of tilapia showed the procedure to be effective. "Two-way analysis of variance (ANOVA) revealed no significant
strain differences (P=0.081; r2=0.106). However, analysis of covariance
with the internal reference strain used as a covariate showed significant
(P=0.049; r2=0.638) strain effects on specific growth (based on standard
length measurements). ... The use of internal reference strain as a
covariate improved the r2 from 0.106 to 0.638 and increased the efficiency
of the test in detecting a true difference." firstname.lastname@example.org
How to identify families when parents have not been well sampled
(parental allocation of singles in open systems): a computer program for
individual parental allocation with missing parents. 2005. URL
Duchesne, P., T. Castric and L. Bernatchez. Molecular Ecology Notes
parental assignment program (using co-dominant markers) is designed to
detect missing parents when not all parents have been sampled. It would be
useful, for instance, in
shrimp breeding where a number of males usually die after reproducing but
before they can be sampled.
Assumptions must of
course be made to achieve this, in particular random mating and
binomially-distributed reproductive success. (The latter assumption
implies an equal probability of producing offspring, but not a strictly
equal numbers of offspring.) The authors say some violation of these
assumptions can be tolerated and the program looks to be useful.
The interface resembles
the familiar PAPA program, by the same authors, where sampling is assumed
to be complete. Both programs can be downloaded from http://www.bio.ulaval.ca/louisbernatchez/links.htm#soft_parent_anal
Estimating effective population size from a single sample
bias correction for estimates of effective population size based on
linkage disequilibrium at unlinked gene loci. 2006. Waples, R. S.
Conservation Genetics 7:167-184.
Effective population size (Ne) is an important
parameter in applied conservation genetics because it is the starting
point for speculation & meditation about the rate of inbreeding and
loss of genetic diversity in small populations. The value of Ne in a wild
population can be estimated in several ways from sample data on neutral
markers such as microsatellites.
One such procedure is
especially useful in that it requires only one sample from the population
rather than two or more samples taken at different times. The value of Ne is inferred from the disequilibrium (lack of random
Mendelian assortment) among alleles at different marker loci within
genotypes. Disequilibrium is a function of Ne.
A companion paper in this
issue of Conservation Genetics (England et al., 7(2), pp. 303-308, email@example.com)
reports that the single-sample estimate of Ne can be severely biased
downwards if the number of
individuals in the sample is smaller than Ne itself.
The paper noted here (Waples) offers several modifications to the
standard calculation, which "effectively eliminate the bias in ... most cases. The modified method also performs well in estimating Ne
in non-ideal populations with skewed sex ratio or non-random variance in reproductive success". firstname.lastname@example.org