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.
540. News flash! repeatable domestication at the molecular level
parallel evolutionary changes of gene transcription profiles in farmed
Atlantic salmon. 2006. Roberge, C., S. Einum, H. Guderley and L.
Bernatchez. Molecular Ecology 15:9-20.
salmon domesticate easily and many generations of cultivation have brought
about significant changes (improvements, from an aquacultural perspective)
in growth rate, behaviour and other traits in hatchery populations around
the world. These changes are sometimes associated with formal, artificial selection but they tend to occur
anyway in well-run hatcheries.
The quantitative genetics of some of the
affected traits (their heritability, dominance, gene interaction etc.) is
understood to some extent. It is also believed that genetic changes which
benefit aquaculture are dangerous to wild populations which come in
contact with domesticated populations.
paper systematically explores, apparently for the first time, the
differences in gene expression between wild and domesticates salmon --
differences in which genes are turned on and which turned off -- and brings our understanding of the domestication syndrome to a level
deeper than the statistical
analysis of phenotypes.
difference in gene expression between wild and farmed salmon is surprisingly large:
"five to seven generations of artificial selection led to heritable
changes in gene transcription profiles, the average magnitude of the
differences being 25% and 18% for at least 1.4% and 1.7% of the expressed
genes in juvenile salmon from Norway and Canada, respectively".
The truly noteworthy discovery was that changes in the transcription profile of
one aquacultural population were often paralleled by changes in the other.
This suggests that domestication is to a considerable degree repeatable at
the molecular level, and therefore potentially understandable at the molecular level.
The discussion of the effect of domestication on
particular transcribed genes, including MHC, is fascinating. See June 2006
#503 for parallel changes in gene expression in isolated wild populations. email@example.com
539. High heritabilities, low genetic correlations in P. monodon
and genetic correlations of growth and survival in black tiger prawn
Penaeus monodon reared in tanks. 2006. Kenway, M., M. Macbeth, M.
Salmon, C. McPhee, J. Benzie, K. Wilson and W. Knibb. Aquaculture
heritabilities of weight-at-age and growth were both high in this
experiment, ranging from 0.3 to 0.7 approximately. Heritability of family
survival in the culture system (with no exposure to disease challenge) had
similar values. Genetic correlations between weight-at-age (or growth) and
family survival were sometimes negative and sometimes positive, but were
always low with large standard deviations.
The genetic correlations were not
significant so there is no evidence of a tradeoff that might cause
trouble, in the absence of disease challenge at least. All of this is good
news for aquaculture selection programs with monodon. firstname.lastname@example.org
538. Inbreeding depression more
serious in bad environments
depression in benign and stressful environments. 2005. Armbruster, P.
and D. H. Reed. Heredity 95:235-242.
expect inbreeding to have a larger effect on survival and fecundity as the
environment deteriorates, and this meta-analysis of 34 published studies
shows that a poor environment usually does increase inbreeding depression.
"Inbreeding depression increases under stress in 76% of cases... .[estimated]
lethal equivalents are significantly greater under stressful (mean=1.45,
median=1.02) than relatively benign (mean=0.85, median=0.61) conditions.
This amounts to an approximately 69% increase in inbreeding depression in
a stressful vs. a benign environment." The survey comprised 11 plant
and 10 animal species. Environmental stresses included toxins,
temperature, starvation, desiccation and competition.
authors observed that different inbred lineages within a population often
differ strongly in their response to inbreeding in stressful environments. email@example.com
537. Heritability of Oreochromis niloticus growth at different ages
genetic analysis of Nile tilapia (Oreochromis niloticus L.) body weight
using a random regression mode. 2005. Rutten, M. J. M., H. Komen and
H. Bovenhuis. Aquaculture 246:101-113.
objective of this study was to estimate heritabilities of tilapia growth
rate at all ages, not just when animals reach harvestable size, the usual
target of selection. Late growth is particularly interesting because the
European market likes large fillets.
authors found that heritability is slightly higher when the animals are
young then when they are older, and that there is a strong correlation of
growth rate at different ages. (Compare #531, below.) For this and other
reasons related to the basic physiology of growth they suggest that
selection may be more efficient if performed early in life.
found that the relative breeding value of the founding populations in the
broodstock changed during the growth period, so choice of founder strain
should depend to some extent on the intended harvestable size. Statistical procedures used in this interesting study go well beyond the
conventional animal model approach to estimating heritability which is now current in
536. Conserving breeds to maximize
scope for selective improvement
novel method for the estimation of the relative importance of breeds in
order to conserve the total genetic variance. 2005. Bennewitz, J. and
T. H. E. Meuwissen. Genetics Selection Evolution 37:315-337.
breeding strategy conserves
the most additive genetic variance, when there is a choice of breeds to be conserved? This simulation uses information on average
kinship within and between breeds, estimated from pedigrees or from marker
data. (June 2006 #493).
results show that the [best
variance conserving strategy] favors
breeds with a high within breed kinship that are not related to other
method suggests conserving breeds that show a large difference in the
respective population mean of a hypothetical quantitative trait. This
maximizes the speed of achieving selection response for this hypothetical
selection direction." See June 2006 #494 for economic aspects of
choosing which breeds to conserve. firstname.lastname@example.org
535. High-male populations of Macrobrachium rosenbergii
of all-male stock by neofemale technology of the Thai strain of freshwater
prawn, Macrobrachium rosenbergii. 2006. Rungsin, W., N. Paankhao and
U. Na-Nakorn. Aquaculture 259:99-94.
giant freshwater prawn Macrobrachium rosenbergii is an important
aquacultural product, especially in Thailand but elsewhere as well. Males
grow faster than females and are more useful for aquacultural production.
This paper describes a technique for producing broods which are largely,
although not completely, male.
First they remove the androgenic gland
from male PLs, which caused them to mature as females. When these females
were subsequently mated with normal males the offspring are mostly males. Fecundity of the
males-become-female parents was normal. As the authors say, "Our
results suggest that the application of the neofemale technology to
produce all-male stock for aquaculture is promising." email@example.com
534. Useful measure of fitness in
wild or managed populations
individual contributions to population growth: evolutionary fitness in
ecological time. 2006. Coulson, T., T. G. Benton, P. Lundberg, S. R.
X. Dall, B. E. Kendall and J.-M. Gaillard. Proceedings of the Royal Society B
interesting new, operational measure of individual fitness is introduced
in this paper, defined as an individual's contribution to population
growth over a standard interval such as a year.
The measurement, which the authors call "de-lifing", consists of
conceptually removing one individual and its offspring from the population
and re-calculating what population growth would have been without it. This
is repeated for the whole population. De-lifed estimates are somewhat
analogous to the jackknifed parameter estimates which are so useful in
The authors discuss many applications, including
selection gradients on quantitative traits, where the de-lifing method
might be superior to conventional fitness measures such as fecundity. One
can imagine that it might be useful when searching for evidence of current
selection on the MHC complex, for example.
The authors confess that you don't
actually have to know everything about every individual in a population to
use their de-lifing method. firstname.lastname@example.org
533. Feeding genes to Oreochromis niloticus
expression in tilapia following oral delivery of chitosan-encapsulated
plasmid DNA incorporated into fish feeds. 2005. Ramos, E. A., L. L. V.
Relucio and C. A. T. Torres-Villanueva. Marine Biotechnology 7:89-94.
delivery into fish is important for transient gene expression, (e.g., DNA
vaccination). Previous studies have generally focused on intramuscular
injection of DNA vaccines into fish. However, this method is obviously
impractical and laborious for injecting large numbers of fishes." The
authors report expression of a reporter gene which was fed to tilapia as
DNA encapsulated in chitosan.
"These results suggest that DNA
vaccines and other constructs can be easily and cheaply delivered into
fishes orally by use of carriers and incorporation into fish feeds." email@example.com
532. Statistical significance of
wild/hatchery fitness comparisons
confidence intervals of relative fitness for a common experimental design. 2005. Kalinowski, S. T. and M. L. Taper. Canadian Journal of Fisheries and
Aquatic Sciences 62:693-699.
intuitively appealing procedure for comparing the reproductive fitness of
animals in the wild is to genotype them (e.g. with microsatellite markers)
and then identify and count their offspring at some later time after
natural reproduction has been completed. A typical motivation for this
type of experiment is to compare the reproductive fitness of two groups,
such as wild vs. hatchery fish. The problem addressed in this paper
is, how do you establish the confidence limits -- test the significance --
of the outcome of such comparison trials?
turns out from simulation that the above experimental design is quite
informative even with modest sample sizes. The paper is interesting for
another reason too: it includes a subtle discussion of the concept
"relative fitness", tied to basic evolutionary theory, in a
fishery context. The focus is on fitness itself, not the causal components
of fitness, but the authors note that "If selection gradients [e.g. for a quantitative trait] are of interest they can be estimated by fitting a curve to a plot of
fitness versus phenotype for the individuals sampled." A computer
program for applying the statistical methods to real and simulated data is
available at http://www.montana.edu/kalinowski/kalinowski_software.htm E-mail firstname.lastname@example.org
531. Different genes affect
fecundity at different ages
trait loci with age-specific effects on fecundity in Drosophila
melanogaster. 2006. Leips, J., P. Gilligan and T. F. C. Mackay.
paper cited above (#537) shows that heritability of growth rate (ratio of
genetic to phenotypic variance) is different at different ages in tilapia.
This is an original piece of work for aquaculture but numerous papers have
looked at age-dependent changes in genetic variance in other kinds of
organisms. This paper on Drosophila goes deeper into the genetic
architecture of age variation in a fitness trait (fecundity).
identified one QTL on the second chromosome and one or two QTL affecting
fecundity on the third chromosome, but these QTL affected fecundity only
at 1 week of age. There was more genetic variation for fecundity at 4
weeks of age than at 1 week of age and there was no genetic correlation
between early and late-age fecundity. These results suggest that different
loci contribute to the variation in fecundity as the organism ages."
that in this system, unlike tilapia, there was no genetic correlation
between the trait values at different ages. But in the organisms featured
in this website there usually is. At the end of their paper the authors
ask questions that are very relevant to domestication and captive
variation result from the action of a different subset of genes
acting on the trait at different ages or does variation arise from
differences in the influence of particular alleles at the same genes with
age? Do physiological changes with age modulate allelic effects on traits
(in a fashion similar to genotype-by-environment interactions)? And if so,
what are the relevant physiological changes that alter these allelic
530. Faster growing trout uses feed
differences in feed efficiency measured as residual feed intake in
individually reared rainbow trout, Oncorhynchus mykiss (Walbaum). 2005. Silverstein, J. T., M. Hostuttler and K. P. Blemings. Aquaculture
geneticists try to develop faster-growing animals, which increases
profit because fast growing animals generate more revenue per unit of time
(or unit of fixed cost). It would also be useful to develop animals which
are more food-efficient, in the sense that they use less food per
unit of growth -- as long as there is no serious negative correlation
between growth rate and growth efficiency.
In practical aquaculture the correlation between growth
and efficiency is often observed to be positive. Faster-growing animals are more food-efficient when they are
harvested, simply because they spend less time reaching standard market
weight and therefore waste less energy on maintenance metabolism. We don't
know much about possible correlations at a deeper physiological (genetic)
level in aquacultural species, although some work has been done in Norway
The usual statistical analysis of correlations between growth rate
and food conversion ratio (FCR) or its inverse, food conversion efficiency
(or ratio), FCE (or FER) is complicated by the fact that all these ratios
have variables in common.
study on 3 trout strains and their hybrids obviates the common-variable
problem by analysing residual feed intake. "Residual feed
intake was calculated as the difference between intake observed and intake
predicted on the basis of a bioenergetics model; a low RFI indicates
greater efficiency." Fish were reared for a fixed time, not to a
authors found significant genetic variation in RFI among the 6 groups, and
furthermore, "Lower RFI was associated with higher growth rates
(r=-0.38, P<0.05) and greater nitrogen retention (r=-0.82
P<0.001)". This is good news. Faster growing trout used feed more
529. Distinguishing the effects of
diversity loss and inbreeding depression
contribution of inbreeding depression and eroded adaptive diversity to
extinction risk in small populations of shore campion. 2006. Vilas,
C., E. San Miguel, R. Amaro and C. Garcia. Conservation Biology
and loss of genetic diversity are not exactly the same thing. Although inbreeding and diversity loss occur together in small populations where the only available mates are close
relatives, the known deleterious effects of inbreeding can be separated,
conceptually as well as experimentally, from the possibly deleterious
effect of low diversity per se (e.g. physiological buffering, scope
for local adaptation etc.). It
is possible to have a diverse, inbred population in which all individuals
self-fertilize but are genetically different from each other.
In this paper just such an experiment was set up
by generating several types of small population with plants from a single,
large outbreeding population. One type, homogenous inbred, consisted of
seed from a single self-fertilized plant. A second type, diverse inbred,
consisted of seeds from many different self-fertilized plants. A third
type, diverse outbred, was a mixture of seeds from crossed parents from
the source population and can be thought of as a control.
survival and seed production rates of the homogenous and diverse inbred
populations were only about half that of the control, indicating that inbreeding depression is a more
serious problem than low diversity per se in this (rather small) field
What is diversity per se supposed to do that's good in this
context? It provides adaptive diversity -- the raw material for adaptation
to different environments. However, even though the grow-out environments
differed among populations, the diverse inbred populations did not do
well, nor was there any observable family X environment interaction. The
authors concluded that inbreeding depression trumped local adaptation in
this case. email@example.com