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.
in adaptation to toxic stress
adaptation and fitness costs in killifish (Fundulus heteroclitus)
inhabiting a polluted estuary. 2003. Meyer, J. N. and R. T. Di Giulio.
Ecological Applications 13:490-503.
The authors collected
killifish (also known as mummichogs)
from the highly polluted Elizabeth river in Virginia and reared the F1 and
F2 generations in the laboratory. Relative to control fish from an
uncontaminated site, both generations of Elizabeth River fish were more resistant to the toxicity of Elizabeth River sediment. They
were also, unfortunately, less resistant to
other stressors including photo-enhanced toxicity and hypoxia,
"suggesting that the changes that have conferred resistance to the
toxicity of the Elizabeth River sediments carry a cost of reduced fitness
in other contexts". See March 2003 #398 for a beautiful study of how
the MHC gene complex in this species has evolved to cope with the unusual
parasites which are found in a toxic environment. firstname.lastname@example.org
425. Heritability can be estimated using microsatellite relatedness, but not
Marker-assisted estimation of quantitative genetic parameters in
rainbow trout, Oncorhynchus mykiss. 2003. Wilson, A. J., G. McDonald,
H. K. Moghadam, C. M. Herbinger and M. M. Ferguson. Genetical Research
papers reviewed here have used microsatellite
markers to estimate the genetic "relatedness" between
individuals in wild or experimental populations, and then proceeded to
estimate quantitative genetic parameters, e.g. heritability of growth,
using the relatedness information. This approach has advantages in
aquaculture, genetic conservation and other situations where pedigrees are
impossible to obtain. The authors of this paper have found, unfortunately,
that statistical power and precision are not among those advantages.
heritabilities of size and spawning traits in three ways (1)
conventionally, by using accurate pedigree records constructed from
microsatellite data on offspring and parents (Danzmann's PROBMAX program),
(2) by using microsatellites to infer full-sib relationships without parental data (Oct 2001 #244) and (3) by using a microsatellite
relatedness estimator (see Sept 2001 #227), which acts as the genetic relatedness
variable required for the analysis (a regression) without
specifying explicitly whether the relatedness is due to full-sib,
parent-offspring, half-sib or other relationships in the pedigree.
It is the third type of estimator which is easiest to apply and is most
enticing for use in poorly controlled populations, such as the start-up of
an aquaculture broodstock (Jan 2002 #283).
As it turns out, the
relatedness estimator (Ritland's, Dec 2000 #142) didn't perform very well
in the Type 3 quantitative genetic analysis, mainly because of
inaccuracies and biases in the estimator itself. The full-sib pedigrees
inferred from markers (Type 2 analysis) did much better, but still not as
well as the control (Type 1) because of frequent ambiguities in deducing
full-sib relationships when half-sibs are also present. This of course is bad news. The authors do note, however, that the
Type 2 and 3 analyses provide genetic information which is qualitatively valid and unlikely to be obtainable in any other way. In fact, as the
authors say, "... in this case reconstructing pedigree under the
assumption that only full-sib family structure was present resulted in
estimates of quantitative genetic parameters very similar to those
obtained when the true complex pedigree was known."
One should note, as well,
that there are many types of relatedness estimator in addition to
Ritland's estimator. Furthermore, algorithms are being developed which can
use markers to infer explicit full-sib relationships nested within half-sibships
(e.g. Thomas & Hill 2002. Genet. Res. 79:227-234). email@example.com
424. Low genetic correlation between
successive growth periods in vannamei
Quantitative genetic parameter estimates for size and growth
rate traits in Pacific white shrimp, Penaeus vannamei (Boone 1931) when
reared indoors. 2003. Pérez-Rostro, C. I. and A. M. Ibarra.
Aquaculture Research 34:1-11.
The rare and useful feature of
this experiment is that the growth of individually tagged
individuals was measured over successive intervals so that growth and size
effects could be separated in the analysis. The experiment generated
full-sib families only, and thus the genetic correlations and
heritabilities are larger than if half-sibs had been used. Although
heritabilities were reasonably high the estimated serial genetic
correlation was negative for linear dimensions and only 0.35 for weight,
giving little support to the idea that one can save time and space in a
vannamei broodstock improvement program by selecting rapidly growing animals early.
An unusual feature of the
analysis was the use of 12-week group weight and density as covariates to
statistically remove common environment effects. One cannot help wondering
whether serial genetic covariances might also have been reduced by this
conditioning of the data (removal of common-cause correlation). firstname.lastname@example.org
423. Big, dominant, male cod
reduce effective population size
Male reproductive competition in spawning aggregations of cod (Gadus
morhua, L.). 2002. Bekkevold, D., M. M. Hansen and V. Loeschcke.
Molecular Ecology 11:91-102.
Groups of cod were
spawned experimentally and the parentage of the offspring sorted out using
microsatellite markers. "Our results show that multiple males
contributed sperm to most spawnings but that paternity frequencies were
highly skewed among males, with larger males on average siring higher
proportions of offspring. It was further indicated that male reproductive
success was dependent on the magnitude of the size difference between a
female and a male." The reproductive success was highly non-normal
(non-Poisson), which would reduce the effective population size of this
"broadcast spawner" well below the census size. Note Jan 2003
#385, in which another broadcast spawner, the New Zealand red snapper, had
a ratio of effective to population sizes of around 0.00001. email@example.com
inbreeding depression, but not very well
Microsatellite measures of inbreeding: a meta-analysis. 2003.
Coltman, D. W. and J. Slate. Evolution 57:971-983.
The two hypotheses about
natural populations being
tested simultaneously here are, (1) individual variation in life history
and morphological traits is associated with variation in inbreeding and (2)
microsatellite data can be used as a surrogate for pedigree records
to estimate the inbreeding of individuals within populations.
unpublished studies on many taxa were pulled together in this meta
analysis. The Pearson correlation coefficient "r" was used to measured the size of
the inbreeding/phenotype relationship. Two measures of genetic
diversity were used, ordinary multi-locus heterozygosity and d2 (the mean
of the squared difference in repeat units between the two alleles at each
Results are interesting. The association
between trait variation and inbreeding inferred from microsatellite variation
is not very large but is larger for life history traits than for morphological
traits. This is consistent with the idea that much of the variation in
traits related to fitness involves dominance and other non-additive
interactions between genes (see Feb 2000 #10). Ordinary
multilocus heterozygosity usually showed stronger association than d2,
suggesting that it may be a better indicator of (short term) inbreeding.
See May 2002 #312 for a theoretical paper which reaches similar
conclusions, and #316 for another data-based study. The authors of the
present paper also found a strong
"publication bias" in favor of significant results which leads
to an overestimate of inbreeding effects in the literature. firstname.lastname@example.org
More evidence that Baltic
salmon populations can resist
Comparative susceptibility of two races of Salmo salar (Baltic
Lule river and Atlantic Conon river strains) to infection with
Gyrodactylus salaris. 2003. Dalgaard, M. B., C. V. Nielsen and K.
Buchmann. Diseases of Aquatic Organisms 53:173-176.
susceptibility of Norwegian and Scottish commercial salmon stocks to the Gyrodactylus skin parasite lead to major losses of aquaculture production.
Two salmon strains in the Indals river (Sweden) and Neva river (Russia)
are already well known to be relatively much more resistant than the eastern Atlantic
stocks. This paper reports on a comparative study of another Baltic stock
from the Lule river in Sweden, which also turns out to be less susceptible
than Atlantic coast salmon to colonization by Gyrodactylus. email@example.com
420. Genetic background modulates
the effect of inbreeding on parasite load
of synergistic interaction between infection and inbreeding in Daphnia
magna. 2003. Haag, C. R., O. Sakwisk and D. Ebert. Evolution
parasite load. Right? Many papers cited here have suggested this, e.g.
Feb 2000 #9, Nov 2000 #137, Apr 2001 #184, Aug 2002 #340, May 2003 #409.
It turns out, though, that genetic background may be sometimes be more
important than inbreeding per se.
The cladoceran Daphnia magna is in many ways a
good model organism for genetic studies because of its rapid generation
time and ability to propagate either clonally or sexually (both
outcrossing and selfing) for many successive generations. These traits
were used here to look at the effect of inbreeding on resistance to two
species of microsporidean parasite. The test was powerful and direct: the
outcome of clonal completion between the descendents of selfed and
outcrossed siblings. As expected, in control experiments where the parasites were not
present, selfed clones almost always lost out to sibling outbred clones.
What is very surprising
is that this was not true in the presence of the parasites! Sometimes the
selfed clones did better. Furthermore, the effect was not always the same
for the two parasite species. So resistance to the parasites was quite
specific, presumably depending on which particular genes were sampled when the
clones were produced. Susceptibility to particular parasites was is not the result of general
"This indicates that, contrary to the
hypothesis that parasites generally lead to a decreased performance of
inbred genotypes, their effect may depend on the genetic background of the
host as well as on the parasite species, and suggests that inbreeding can
lead to reduced or increased resistance to parasites." See April 2001
#180 for a related paper which showed genetic variation in parasite
resistance in natural populations of Daphnia, and May 2003 #402 for
similar variation among inbred lines of Drosophila. firstname.lastname@example.org
419. A crucial conservation
parameter can be estimated
The power of experiments for estimating relative reproductive
success of hatchery-born spawners. 2003. Hinrichsen, R. A. Canadian
Journal of Fisheries and Aquatic Sciences 60:864-872.
The genetic effect of stock supplementation depends on how successful the hatchery fish
are at breeding in the wild, relative to wild fish. This paper tries to
establish how hard it is to estimate relative success, in the real world.
The author simulates a salmon population which conforms to the familiar
Ricker stock-recruitment relationship. The wild component of the
population is supplemented to varying extents with hatchery-bred fish, and
the question asked is how much work is required to prove that the
reproductive success of hatchery females is different than wild ones. Or
more precisely, what kind of experiment will maximize "the
probability of rejecting the null hypothesis that the reproductive
successes of hatchery- and wild-born spawners are equal when they are not.
This probability is defined as power".
Variables included in the simulation included "the length of
experiment, schedule of hatchery-born spawner introduction, stock
productivity, spawner abundance, interannual variance in production,
fraction of spawners and recruits sampled, and true values of [relative reproductive success] ."
Likelihood functions were derived for analyzing the simulated data.
Results are encouraging. "The power analysis suggests that reliably estimating
reproductive success of hatchery-born spawners relative to their wild-born
counterparts is possible with just a few brood years of spawner–recruit
data, and that choosing a population that has large spawner numbers and
high productivity may decrease the number of brood years required."
The author adds an
important caveat about experiments in the highly-politicized world of
stock supplementation, aquaculture escapes etc. "In all experiments
of which I am aware for salmon populations. (including the experiment
analyzed in this paper), relative reproductive success of hatchery-born
spawners is not measured against reproductive success of wild-born
spawners without supplementation, which, I believe, is the appropriate
baseline. This is the baseline necessary to understand how a population
would perform in the absence of supplementation."
See #416 below, Nov
2000 #130 for an experimental study of relative reproductive success, and
Feb 2002 #287 for inferences based on microsatellite time series in
stocked rivers. email@example.com
418. DNA test for local ancestry in
a re-introduction program
. 2003. Hofkin, B. V., A. Wright, J. Altenbach, K.
Rassmann, H. M. Snell, R. D. Miller, A. C. Stone et al. Conservation
This is an interesting
use of museum DNA samples to solve a practical conservation problem. More
than 150 years after Darwin's visit the Galapagos islands are still a
hotbed of evolution and evolutionary research. One of the islands, Baltra,
lost its population of land iguanas in the late 1940s, and there is an
intention to start the population up again. But where should the
replacement stock come from? Another island which was stocked from Baltra
decades ago would seem a logical source, but there are suspicions that
this island may also have been stocked from other sources. (Apparently it
was decided that any increase in evolutionary potential which might be
achieved by using mixed stock for a re-introduction would not be a Good
Thing relative to the potential loss of local adaptation.)
So, using DNA from museum
specimens collected from several Galapagos islands way back in 1905, the
authors were able to identify animals with cytochrome B haplotypes which
are "unambiguous Baltra origin ....These results provide scientific
criteria for the ecological restoration of these endangered
reptiles." The unambiguous Baltra origin is presumably through the
female line only. firstname.lastname@example.org
417. The trout marker map gets
bigger and more dense
A consolidated linkage map
for rainbow trout (Oncorhynchus mykiss). 2003. Nichols, K. M., W. P.
Young, R. G. Danzmann, B. D. Robison, C. Rexroad, M. Noakes, R. B.
Phillips et al. Animal Genetics 34:102.
The authors report the
updating of their linkage map, which represents the state-of-the-art for
map for species of
aquacultural importance. The
markers now total "1359 genetic markers and the sex phenotype
including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR,
38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four
allozymes". The markers fall into 30 linkage groups.
interesting that AFLP markers may be growing more useful for this sort of
work than microsatellites even though they are dominant markers (see also
March 2002 #310, May 2003 #404). email@example.com
416. Sea-ranched trout may be
swamping a wild population
Lack of molecular genetic divergence between sea-ranched and
wild sea trout (Salmo trutta). 2003. Palm, S., J. Dannewitz, T. Järvi,
E. Petersson, T. Prestegaard and N. Ryman. Molecular Ecology 12:2057-2071.
microsatellite and allozyme study of a supportive breeding program in the
Dalälven river (Sweden) demonstrates that the hatchery has a profound
genetic impact on the wild stock -- one-way gene flow may be around 80% per
A key feature of the supplementation program is that only
fish which are produced in the hatchery and succeed in
returning to the river are used as spawners in the hatchery. Thus
domestication selection for reproducing in the hatchery operates in tandem with selection
for survival in the wild. Although some returning hatchery
fish also spawn naturally in the river no wild genes have been introduced
into the hatchery stock (which was founded with Dalälven fish) since the
late 1960s. It has been a completely closed stock with a sea-ranching
selection component, for about seven generations.
Other studies have
demonstrated genetic and even morphological differences between wild
and hatchery Dalälven trout. This study, on the other hand shows, that the
difference between stocks in a single year is no greater than the
year-to-year variation within the two stocks; i.e. there is no persistent
stock difference. The authors infer from their analyses that hatchery and
wild fish have about the same reproductive success in the wild (see #419
above). This is important and would appear to be very good news from a
genetic conservation perspective since it implies that the hatchery should
not be reducing the fitness of the wild component of the population, despite
the fact that natural reproduction is not selected during the sea-ranching
phase (at least, not directly; selection for wild survival may counter
selection for hatchery reproduction).
The authors point out,
however, that after 30 years of intensive supportive breeding with this
high level of introgression, the "wild" Dalälven fish can
hardly be the same as they were when the program started. The same point
is made in #419 above. firstname.lastname@example.org
415. Adaptation to acid environment
is partly through the mother
Geographic variation in acid stress tolerance of the moor frog,
Rana arvalis. I. Local adaptation. II. Adaptive maternal effects. 2003.
Räsänen, K., A. Laurila and J. Merilä. Evolution 57:352-362.
The authors compared
early life history traits of frogs collected from highly acidified
environments with frogs from well buffered, neutral environments, and also
looked at the reciprocal crosses between the two types of population. Sure
enough, when tested in an acid environment, the offspring of animals from
acid environments had superior survival and hatchling size and weight. An interesting finding in this study
(also see Part II, ibid 363–371) is a strong maternal effect on
survival, through the structure and composition of the gelatinous egg
capsule. Unfortunately, the experimental design could not separate
environmental from heritable maternal effects.
Another example of a
maternal effect which is important in aquaculture and which may involve a heritable maternal effect is the correlation
between egg size and offspring growth. That particular maternal effect,
egg size, should be taken into
account in selection programs where growth is the objective, especially if there is
also a tradeoff between female growth and female investment in egg size. email@example.com
414. White shrimp genetically
uniform over its range
Population genetic analysis of white shrimp, Litopenaeus
setiferus, using microsatellite genetic markers. 2003. Ball, A. O. and
R. W. Chapman. Molecular Ecology 12:2319-2330.
The white shrimp is
endemic to the east coast of North America, from the Carolinas into the
Gulf of Mexico. This
microsatellite study (6 loci) found that the shrimp in the Atlantic were
slightly but significantly different from those in the Gulf. Some weak
local differentiation within these broad groupings was also observed but
the authors conclude that this is largely "short-term sampling
effects rather than persistent genetic differences". Deviations from
Hardy Weinberg distributions were observed but attributed to null alleles,
not gametic disequilibrium due, e.g., to population fluctuations.
On the whole, there is
considerable genetic homogeneity over the whole range, probably because of
the pelagic spawning and planktonic dispersal phases of the life cycle.
"The major findings of this study were the consistency of allele
frequencies over time, sporadic differentiation among neighbouring
locations indicative of the effects of high reproductive variance, and
slight but significant differentiation between the Gulf of Mexico and the
Litopenaeus setiferous appears to shows less
regional differentiation than Penaeus monodon or P. stylirostris.
The authors estimated long-term effective population sizes in the
millions, but the sporadic, local fluctuations are intriguing and may have
adaptive and evolutionary implications (e.g. Nov 2001 #259). firstname.lastname@example.org
413. A useful shrimp population
of mitochondrial control region in population genetic studies of the
shrimp Penaeus. 2003. Chu, K. H., C. P. Li, Y. K. Tam and S. Lavery.
Molecular Ecology Notes 3:120-122.
"This study reports
a primer set for amplifying a partial fragment of about 610 bp in the fast
mutating mitochondrial control region in shrimps of the genus Penaeus [merguiensis] (Decapoda:
Penaeidae). ... The results indicate that the mitochondrial control region
provides more informative sites and reveals more haplotypes [than
other mt sequence and RFLPs] , making it most useful for evaluating genetic
variations within and between populations of Penaeus species." email@example.com
412. Identify any species with one
Novel universal primers establish identity of an enormous number
of animal species for forensic application. 2003. Verma, S. K. and L.
Singh. Molecular Ecology Notes 3:28.
describes a polymerase chain reaction (PCR)-based approach, which .... is
able to reveal whether the source of the sample is human or animal, and,
if animal, which of the 221 animal species included in the study, simply
by using one set of novel primers... The primers described in this study
universally amplify a specific segment of mitochondrial cytochrome b
sequence from a sample of unknown origin and delineate its identity to the
level of family, genus and species...." firstname.lastname@example.org