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.
588. Molecular adaptive
evolution in lake whitefish
Integrating QTL mapping and
genome scans towards the characterization of candidate loci under parallel
selection in the lake whitefish (Coregonus clupeaformis).
2005. Rogers, S. M. and L. Bernatchez. Molecular Ecology 14:351-361.
Lake whitefish coexist in two forms, dwarf and normal, in many Canadian
lakes. At the ecological level, the selective forces involved in
maintaining the two sympatric ecotypes (assumed to be "adaptive
peaks") are reasonably well understood. Bernatchez’s laboratory has
previously reported on parallel changes in the expression of genes in
geographically isolated lakes (June 2006 #503) and aquacultural salmon
populations (Sept 2006 #540). In this new paper, the stable and repeatable
(among lakes) adaptive divergence is used as a starting point for a study
of selection at the molecular
Several procedures are
involved in the genome scan procedure: hybridization and back-crossing of
ecotypes, scoring and mapping numerous marker loci (AFLP in this case),
looking for statistical associations between the inheritance of markers
and variation in growth. This identifies markers for growth QTL. All this
is step one.
Step two is analysis of
the distribution of genetic distances among the markers. Outliers from the
distribution are, by definition, not part of a population of random
(neutral) markers and are affected by something else, probably selection.
The logical path is completed by observing that, sure enough, the outliers
are QTL for growth. Selection on growth is understood at the ecological
level, as already mentioned.
"We found evidence
of significantly high levels of molecular divergence among eight growth
QTL where two of the strongest candidate loci under the influence of
directional selection exhibited parallel reductions of gene flow over
This paper is also
interesting because one can also think of it as way of measuring
evolutionarily significant divergence among populations. Sets of neutral
markers, such as microsatellites, are normally used to measure divergence,
but it is known that the correlation between neutral and quantitative
genetic diversity is very low.
Genetic distances based
on outliers might be more useful, as suggested long ago by R.C. Lewontin
and J. Krakauer. The distribution of neutral markers is affected by
demographic processes at the level of the whole genome, while selection
affects particular QTL and their neighboring markers. Outlier-based FST and GST statistics would be useful, for example in identifying
populations worthy of conservation or even for incorporating in a
selective breeding program. Louis.Bernatchez@bio.ulaval.ca
587. Tilapia responds well to selection in extensive aquaculture systems
estimates and response to selection for growth of Nile tilapia
(Oreochromis niloticus) in low-input earthen ponds. 2006. Charo-Karisa, H., H. Komen, M. A. Rezk, R. W. Ponzoni, J. A. M. van
Arendonk and H. Bovenhuis. Aquaculture 261:479-486.
species show a lot of promise for low-input (i.e. sustainable)
aquacultural systems. Can their profitability in such environments be
increased through the magic of
genetics? In this experiment covering two generations, O. niloticus was
grown in ponds fertilized with chicken manure without added feed.
"Heritability estimates for BW ranged from 0.38 to 0.60, and the
heritability for survival ranged from 0.03 to 0.14.The estimated selection
response was 23.4 g (34.7%) between G0 and G1 and 13.0 g (14.9%) between
G1 and G2.
These results demonstrate
the feasibility of selection for growth of tilapia in low-input environments." Selection was based on
estimated breeding values in a fully-pedigreed population. See #580, below
for more tilapia selection results. Hans.Komen@wur.nl
586. The right way to test for WSSV
of experimental infection protocols for the estimation of genetic
parameters of resistance to White Spot Syndrome Virus (WSSV) in Penaeus
(Litopenaeus) vannamei. 2006.
Gitterle, T., B. Gjerde, J. Cock, M. Salazar, M. Rye, O. Vidal, C. Lozano
et al. Aquaculture 261:501-509.
two procedures tested were (1) individual, oral administration of WSSV
virus in a liquid medium and (2) mixing infective medium into the water
the shrimp were swimming in.
Both procedures were designed to ensure that all animals were exposed at
the same time to the same concentration of virus. (Standard challenge
tests do not ensure this.) The statistical procedure was a type of
time-to-die analysis as recommended by the authors in an earlier paper
(which is not identical to this one; July 2006 #516). Several batches of full- and half-sib families were used.
were zero or very low in both challenge procedures. Cumulative mortalities
were high -- exceeding 80%. Even
with these careful challenge protocols the time course of cumulative
mortality was similar at all dosage levels once the infection took hold --
in other words, mortality was dominated by contagion within the tanks. The
authors ascribe this, no doubt correctly, to high population density.
My personal conclusion is
that even with the most careful experimental and statistical protocols,
such as those used here, challenge tests in groups provide no meaningful quantitative genetic information. They may be of some use in practice for brute-force
selection of survivors. Statistical assumptions of independence are
hopelessly invalid and I don't know of any models that can handle a
contagion-induced error covariance added to the genetic covariance among
the tested individuals. (If someone else does, I would love to be
instructed.) In the mean time
we need a better way of evaluating WSSV resistance. email@example.com
585. How well can you infer
pedigrees from molecular markers in wild populations?
of marker-based relatedness estimators in natural populations of outbred
vertebrates. 2006. Csilléry,
K., T. Johnson, D. Beraldi, T. Clutton-Brock, D. Coltman, B. Hansson, G.
Spong et al. Genetics 173:2091-2101.
paper examines the frequency of two kinds of errors in marker-based
pedigrees: "first, misclassification rates between pairs of genetic
relationships and, second, the proportion of variance explained in the
pairwise relatedness estimates by the true population relatedness
composition (i.e., the frequencies of different relationships in the
The conclusion is
interesting: the frequency of errors (i.e. the performance of a
marker/analysis system) depends to a large extent on the nature of the
relationships within the population. Specifically, when the variance of
relatedness in a population is low, as will frequently be the case
especially when most pairs have no common ancestors within the last couple
of generations, the ability of relatedness estimators to estimate specific
pairwise relationships correctly is also low.
conservation breeding, where the objective is to mate unrelated
individuals, these errors are in the right direction because relatedness
is overestimated. But when the objective is to identify highly related
individuals, perhaps to see whether they avoid mating with each other or
their offspring have more parasites, relatedness is underestimated in many
More generally, when the
variance of relatedness is low, very little of it is explained by variance
in the relatedness estimators. The explanatory power of the estimator is
therefore low when it is used as an explanatory variable in regression or
a categorical variable in ANOVAs. Discouraging. See also Dec 2006 #572. firstname.lastname@example.org
584. Gene expression and development of precocious male salmon
life histories shape brain gene expression profiles in males of the same
population. 2005. Aubin-Horth,
N., C. R. Landry, B. H. Letcher and H. A. Hofmann. Proceedings Royal
Society (B) 272:1655-1662.
certain proportion of Atlantic salmon males become sexually mature at a
small size and, instead of migrating to the sea, hang around in fresh
water on the lookout for whatever opportunities sally by -- the
"sneaker" reproductive strategy. Sneaking works as a component
of a mixed strategy, is provably adaptive and varies considerably from
stream to stream. It causes a severe problem in aquaculture, however,
because the sneaker phenotype has little commercial value.
In this paper gene
expression profiles of mature sneaker males are compared to those of
juvenile males of the same age (i.e. males which will mature after going
to sea) and also to females. The authors found that "roughly 15% of
the genome varies in gene expression in the brain between the two male
Genes known to be
associated with reproduction tended to be up-regulated in the sneaker
phenotype, as was the circadian clock gene. Most interestingly, the
expression profile of the sneaker was closer to the female than to the
immature juvenile male, which the authors interpret as supporting the
idea of Thorpe and others that males that grow more slowly, and fail to
reach a threshold size, respond by actively repressing maturation and
going on to develop the anadromous phenotype.
expression patterns in immature males were different both from immature
females and sneakers, indicating that delayed maturation and sea migration
by immature males, the ‘default’ life cycle, may actually result from
an active inhibition of development into a sneaker." See Nov 2006
#559 for size/growth effects on maturation. email@example.com
583. Ontario walleye are genetically okay
outbreeding and environmental effects on genetic diversity in 46 walleye
(Sander vitreus) populations.
2006. Cena, C. J., G. E. Morgan, M. D. Malette and D.D. Heath. Molecular
Ontario (Canada) walleye populations were studied to find the relationship
between life history traits related to growth, reproduction and mortality
and measures of genetic diversity (heterozygosity, d2, and F). Only one
relationship was found to significant in both sexes: "Walleye early
growth rate was the only life history trait significantly correlated with
population heterozygosity in both males and females." The authors
conclude that "the weak relationships between genetic diversity and
life history traits indicate that inbreeding and outbreeding depression
are not yet seriously impacting Ontario
walleye populations." firstname.lastname@example.org
582. Model of evolutionary
adaptation to domestication
potential model system for studying the genetics of domestication:
behavioral variation among wild and domesticated strains of zebra danio
(Danio rerio). 2005. Robison,
B. D. and W. Rowland. Can. J. Fish. Aquat. Sci. 62:2046-2054.
domesticated zebra fish studied here have been adapting to laboratory
environments for at least 24 generations and the wild strain (from India) for only four. No selective harvesting has been taking place, i.e. this
is not a model of evolution to a fishery (compare with July 2006 #508).
The lab zebra fish were less fearful, spent more time at the surface and
grew faster than the wild strain. As the authors point out, zebra fish
would seem to be an excellent model for the study of domestication. The
evolutionary changes are similar to those in salmonids, carps and -- with
the likely, important exception of growth rate -- tilapia. (See Jan 2003 #383)
"The availability of a
complete genome sequence [for zebra fish], saturation mutagenesis screens, and a dense
genetic map will allow identification of the genetic targets of
domestication selection.... [which can be] tested as candidate genes in
other species." email@example.com
581. Poor nutrition increases
variation among inbred (not outbred) families of oysters
of dietary restriction during juvenile development on adult performance of
Pacific oysters (Crassostrea gigas). 2006.
Evans, S. and C. Langford. Aquaculture 259:124-137.
article recently cited here (Nov 2006 #559) showed that in cultured
salmon, juvenile environment has a strong effect on the rate of growth
later in life. Is this true of cultured oysters as well?
This study shows
that final body weight and survival differed among outbred families (i.e.
there is genetic variation in the families tested) but that feeding level
in the nursery did not have much effect. The situation was rather
different among inbred families (full- or half-sib mating) when
nutritional stress reached a high level. "Significant rank changes
among inbred families for both individual body weight and yield occurred
only among families reared under the most stressful nursery feeding
This seems rather important, given the high probability of
accidental inbreeding in bivalve hatcheries. If production in one season
comes mainly from one or two families, and they happen to be
inbreeding-sensitive, the broodstock would suffer a permanent decline in
yield. (Permanent, that is, unless domestication selection eventually
purges the deleterious recessives, which can happen under certain
580. Good selection response in
GIFT tilapia in Malaysia
parameters and response to selection for live weight in the GIFT strain of Nile tilapia (Oreochromis niloticus).
2005. Ponzoni, R. W., A. Hamzah, S. Tan and H. Kamaruzzaman. Aquaculture
useful report on the GIFT strain in Malaysia describes a selection experiment based on
estimated breeding values (BLUPs). The realized response to selection was
around 10% and was estimated in several ways, including comparison with a
control. Good. Putting this information together with other recent
experiments (e.g. #587, above) it seems likely that 10% is a reasonably
safe figure to expect for genetic gain in tilapia, supposing a moderately
diverse broodstock and a reasonably well-run program. (Personally,
however, I err on the safe side and use 6% in cash flow models of
broodstock development with
a 10-year planning horizon.). firstname.lastname@example.org
579. WSSV genes have lower
expression at higher environmental temperature
modifies gene expression in subcuticular epithelial cells of white spot
syndrome virus-infected Litopenaeus vannamei. 2007. Reyes, A., M. Salazar and C. Granja. Developmental &
Comparative Immunology 31:23-29.
is widely recognized that low temperatures increase the rate of mortality
from viral infection in Litopenaeus vannamei. In this experiment the
differential expression of WSSV genes in infected vs. non-infected shrimp
was observed at 26°C and 33°C through the use of subtractive suppressive
hybridization and real-time PCR.
Sure enough, there was greater expression
of WSSV genes at 26°C. At the higher temperature expression was reduced
and mortality from WSSV was completely suppressed. This study helps answer
the question whether high temperature improves the immune response of the
shrimp (e.g. by increasing the rate of apoptosis) or directly affects the
functioning of the virus. The
shrimp genes differentially expressed in infected vs. uninfected
individuals were not much affected by temperature, unlike the WSSV genes.
So the authors conclude that "... our results show that the main
effect of hyperthermia on subcuticular epithelial cells is to reduce the
expression of WSSV genes rather than to induce host genes that might
contribute to control the infection." Note that subcuticular
epithelial cells are the main target of WSSV. email@example.com
578. Statistical power analysis for genetic distance
POWSIM: a computer program for assessing statistical power when testing
for genetic differentiation. 2006.
Ryman, N. and S. Palm. Molecular Ecology Notes 6:600-602.
analysis of genetic differentiation among postulated genetic groups, based on
genetic markers, should include an indication of the statistical power of
the analysis both to detect differences which really exist, and to avoid
imputing population structure where there really isn't any.
program uses a Monte Carlo approach to generate a power analysis and
also estimates errors for Fisher's exact test and chi-square test of the
"no difference" null hypothesis. The POWSIM program can be
downloaded from http://www.zoologi.su.se/~ryman . POWSIM should be useful for planning how many markers and samples are
needed for having a fair go, as the Australians say, at finding something
Perhaps more often, it can be used "...in studies where
no significance has been obtained ... to evaluate the magnitude of true
differences that may have gone unnoticed, given the particulars of the
investigation conducted". The hypothetical true level of
differentiation among sample groups is specified as FST in the
simulation. Various combinations of sample number, number of marker loci,
allele frequency distributions can be specified to match the particulars
of the (proposed) investigation. It should be noted that the null
hypothesis being evaluated is, specifically, that there is no significant
differentiation caused by random drift without mutation, selection or
577. Clear genetic evidence of
hatchery genes moving into wild salmon populations
immigration from compensatory hatchery releases into wild Atlantic salmon
population in the Baltic
spatio-temporal analysis over 18 years.
2005. Vasemägi, A., R. Gross, T. Paaver, M.-L. Koljonen and J. Nilsson.
The rate of
immigration from hatchery stocks into one of the largest wild, riverine
salmon populations in the Baltic region is estimated in this paper. Fish
are released from hatcheries into other rivers for stock supplementation.
The overall immigration rate
into the non-supplemented population averaged a bit less than 10% but was
as high as 25% between 1993 and 2000. The hatchery stocks were definitely
straying into the natural system. Furthermore,
there has been a decline in Fst in the joint analysis of the natural and
supplemented population which the authors interpret as evidence for
genetic homogenization, i.e. introgression of hatchery genes into the wild
gene pool. firstname.lastname@example.org