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.
528. Domarker-based paternities
estimate heritability well enough to be useful?
How do misassigned paternities
affect the estimation of heritability in the wild? 2006. Charmantier, E. and D. Réale. Molecular Ecology
In this simulation study
the effect of mis-assignment was actually not too bad. Furthermore -- and
this is beneficial in most studies -- the effect is to underestimate heritabilities. "These analyses suggest that the bias induced by
misassigned paternities on heritability estimation depends on the level of
heritability and the rate of paternity error. Typical rates of extra-pair
paternities in birds (around 20% of offspring) should result in an
underestimation of heritability of less than 15% when estimated over a
minimum of 100 broods." email@example.com
527. Vannamei candidate genes for
growth don't actually affect growth
SNP analysis of
AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp. 2005. Glenn, K. L., L. Grapes, T. Suwanasopee,
D. L. Harris, Y. Li, K. Wilson and M. F. Rothschild. Animal Genetics
authors studied two candidate genes for growth in shrimp, one (AMY2)
believed to affect digestive function and the other (CTSL) the intermolt
cycle. Several single nucleotide polymorphisms (SNPs) were found to be
segregating in a study population of Kona line P. vannamei. There was,
however, no significant association between variation in growth rate and
variation in the growth- and digestion-related candidate genes in this population.
The experiment was very small, as the authors point out. The negative
result might be an instance of the possible inefficiency of candidate gene
studies in general, as proposed in June 2006 #500. firstname.lastname@example.org
different mating designs on inbreeding, genetic variance and response to
selection when applying individual selection in fish breeding program. 2006.
Dupont-Nivet, M., M. Vandeputte, H. P. and B. Chevassus. Aquaculture
useful simulation suggests how to mate fish or crustaceans, in an
aquaculture selection program, so as to minimize long-term inbreeding. It
is known that the best procedures use pedigree data and arrange matings
based on kinship . But in practical aquaculture pedigrees are
often not available so what can one do?
In this simulation,
factorial designs (s sires each
mated to d dams producing s*d families) worked
better than nested designs (each sire mated to a different set of N dams, producing s*N families, which were
better than pairwise matings. "When possible, partial factorial
mating (FS) designs seemed to be a good compromise to achieve high genetic
responses while preserving genetic variability." A paper noted in
Mar-April 2004#476 reaches similar conclusions. Of course, the more
families the better.
that in accord with general theory this simulation shows that the
arrangement of matings does not make a large difference in inbreeding over
the long term, other things being equal. In practical aquaculture,
however, the avoidance of short-term inbreeding may be of crucial
importance to production. Also, mating strategies often have intellectual
property protection as a primary objective. email@example.com
525. Tilapia salinity tolerance
Salinity tolerance in superior
genotypes of tilapia, Oreochromis niloticus, Oreochromis mossambicus and
their hybrids.2005. Kamal, A. H. M. M. and G. C. Mair. Aquaculture 247:189-201.
the genotypes (strains) tested in these experiments grew faster at higher
than at zero salinities, the highest tested being 30 ppt. "The hybrids
revealed high average positive heterosis for weight gain (1.24) and
biomass gain (1.33) but less for FCR (1.08)."
The niloticus-mossambicus hybrid definitely out-performed either pure species. "The
hybrid would be particularly recommendedat
salinities above 20 ppt where the survival of O. niloticus can be
compromised." Interesting. The authors also suggest that
"perhaps the most likely application of hybridization would be in
developing specific combinations of commercially valuable traits."
(See May 2002#321 salinity-tolerance gene.) firstname.lastname@example.org
524. Maximizing heterozygosity also
maximizes allele diversity
individuals' contributions to maximize the allelic diversity maintained in
small, conserved populations. 2004. Fernández, J., M. A. Toro and A. Caballero. Conservation Biology
diversity-conserving breeding plans focus on inbreeding or heterozygosity [GD]. (See July 2006#512.) However, the
total number of alleles at a locus [AD] is a more sensitive indicator of
genetic drift, and it might be
argued that allele number is a better indicator of long-term evolutionary
potential too. (See June 2004#480 breeding scheme that maximizes AD.)
So, considering these two
strategies together, what effect does maximizing GD have on allele number?
The author's computer simulation shows that "strategies that maximize
GD, by managing contributions from parents, keep levels of AD as high as
strategies maximizing AD itself, for a wide range of situations including
different numbers of molecular markers used and the possibility of
evaluating a number of offspring per parent to make decisions. Because
maximization of GD also minimizes levels of inbreeding, this should be the
strategy of choice in any conservation program." (Apr 2004#473 on
equal contribution breeding schemes.) email@example.com
523. Spawn number is heritable in
the categorical trait ‘number of spawns’ in Pacific white female
shrimp Penaeus (Litopenaeus) vannamei.
2005. Ibarra, A. M., F. G. Arcos, T. R. Famula, E. Palacios and I. S.
Racotta. Aquaculture 250:95-101.
study population had been domesticated in Venezuela and then in Mexico
under the name "Megalos". The authors used a mixed-model
analysis of two generations of full-sibs, mothers and daughters.
"Phenotypes were reordered for each of 5 categories: 0, 1, 2, 3, and
4 or more spawns. Heritability of spawn numbers was 0.20, with a 95%
confidence interval of 0.06–0.43, indicating that this trait can be
improved by selective breeding." (See Apr 2004#477.) firstname.lastname@example.org
522. Gene flow may enhance a search
effect on the genetic architecture of a local adaptation and its
consequences for QTL analyses.
2006. Griswold, C. K. Heredity 96:445-453.
find a quantitative trait locus (QTL) there must be at least two alleles
segregating at that locus in the group of animals being studied. QTLs are
more interesting and easier to find when substituting one allele for
another has a large effect on the trait.
This computer simulation
looks at the properties of QTLs that evolve in two populations that
are adapting to different local conditions and exchange genes by
migration. The question is,
how does the genome evolve when adaptive, divergent adaptation is swamped
by gene flow? A common situation in genetic conservation and aquaculture.
The problem has been addressed at the population-genetic-theoretic level
for 70 years but now we have the tools to look at the evolution of the architecture of the genome.
paper uses computer simulations to quantify the genetic basis of local
adaptations when there is gene flow versus when populations are isolated.
It then takes samples from the two locally adapted populations to form
mapping populations that may be used in a QTL experiment."
details of the simulation reported here are sensitive to migration rate
and selection pressure in a rather complicated way, as one might expect.
But the bottom line is interesting: "Gene flow between populations
that are used in a QTL study tends to cause the average magnitude and
percent variance explained (PVE) of an allele in a mapping population to
increase." They also found that the effect on QTL was largest when
the divergence was less than ancient (say 1000 generations) and the
populations had not reached their different optima, i.e. were not
experiencing stabilizing selection.
are obvious implications here for choosing a population to use for QTL
mapping, and anyone with the freedom to make such a choice should look at
the paper carefully. email@example.com
populations as a genetic resource in a changing climate?
Life on the edge:
the long-term persistence and contrasting spatial genetic structure of
distinct brown trout life histories at their ecological limits. 2006. Antunes, A., R. Faria, W. E. Johnson, R. Guyomard and P. Alexandrino.
Journal of Heredity 97:193-205.
trout have persisted on the Iberian peninsula, at the southern limit of
their temperature range, since the region was a glacial refugium tens of
thousands of years ago. This
allozyme & microsatellite study of 20 populations documents a genetic
story that accords very well with modern micro-evolutionary theory.
populations display the genetic signatures of less-stable population sizes
than populations farther north. Southern populations have relatively low
within-population genetic diversity owing to bottlenecks and drift, but
the overall diversity is high indicating that the small populations are
not historically young (they have some private alleles).
data [suggest] ... that careful
interpretation of the evolutionary history of glacial refugia is
necessary, especially where populations persisted for a long time but not
always with optimal ecological conditions. These peripheral populations
are of high conservation value and should be preserved to help conserve
the future potential of the species." This remark probably has a
general validity. If and when the climate warms, the genetic adaptations
of southern extreme populations may
become the key to species survival over large areas. Contrast this story with Jan-Feb 2004 #464 which describes a meta-population of brown trout living well within their ecological comfort zone, in
Denmark, where sub-populations frequently disappear and then re-appear
again by recolonization and thus have no particular value from a genetic
conservation viewpoint. firstname.lastname@example.org or email@example.com
520. Desirable and undesirable
correlates of body weight in salmon
Development of an
Atlantic salmon (Salmo salar) genetic improvement program: Genetic
parameters of harvest body weight and carcass quality traits estimated
with animal models. 2005. Quinton, C. D., I. McMillan and B. D. Glebe. Aquaculture
canthaxanthin & colour were all found to be moderately heritable in
Atlantic salmon and the genetic correlation with body weight was positive
-- which is good news for aquaculture selection programs. But the genetic
correlation between weight and fat was also positive, which, while not
unexpected, is bad news nevertheless. firstname.lastname@example.org
519. Matched rates of inbreeding in
control and mass-selected tilapia lines
during mass selection for growth in Nile tilapia, Oreochromis niloticus
(L.), assessed by microsatellites.
2005. Romana-Eguia, M. R. R., M. Ikeda, Z. U. Basiao and N. Taniguchi.
Aquaculture Research 36:69-78.
four generations of selection, the levels of inbreeding and heterozygosity
in the selected line changed over time in the expected directions, i.e.
downwards. What is interesting is that the control line also changed; in
fact allelic diversity at 5 microsatellite loci was slightly but
non-significantly lower in the control.
The parallel changes in
the selected and control lines is presumably because the control in this
experiment was actually centrally-selected, not random (collimation; Feb
2002 #293). Central-selection, or collimation, thus appears to be
successful in controlling for inbreeding effects. Since control and
selected lines are matched in their inbreeding, the effect of selection on
growth, survival etc. can be observed separately from inbreeding in
non-pedigreed mass selection programs.
The history of the
current Philippine tilapia strains (GIFT, GIFT-Genomar Supreme, GMT, FaST,
GET-EXCEL, SEAFDEC, Chitralada) is briefly and usefully reviewed in this
paper. email@example.com or firstname.lastname@example.org
518. Cause of spurious
disease-marker correlations in aquaculture
population-genetic model for the production by population structure of
spurious genotype–phenotype associations in discrete, admixed or
spatially distributed populations. 2006. Rosenberg, N. A. and M. Nordborg.
do we often find a "marker" for a trait such as disease
resistance in an aquacultural broodstock, only to be disappointed when the
marker doesn't work in the next generation? It is due to a very familiar
statistical problem -- a common factor produces a spurious correlation
between two variables.
What we want to
find is either a gene which causes an animal to resist a disease (direct
correlation), or a marker gene which is so strongly linked to a resistance
gene that the two stay together down the generations (indirect correlation
where the common factor is physical proximity on a chromosome).
What we much more often find,
however, is a marker/disease association within a mixed group of
individuals from different families or groups of families. The confusing
common factor is the (sub-) population of origin. Sub-populations may have
different allele frequencies at thousands of loci. If the sub-populations
also differ somewhat in their resistance to disease, there will be
thousands of spurious "marker" loci that are labels for the
entire genome of the resistant sub-population, not just the tiny part of
the genome responsible for disease resistance.
It takes several
generations of mixing and segregation for the indirect association caused
by population structure to disappear through random mating. Research on
QTLs (direct causal correlation) or marker-assisted selection (MAS;
indirect correlation by close linkage) will use sophisticated breeding
strategies to find non-spurious correlations in two or three generations.
paper introduces "a general model of spurious association in
structured populations, appropriate whether the population structure
involves discrete groups, admixture among such groups, or continuous
variation across space." The presentation of the theory is technical
but the introduction and discussion are illuminating and well-written
explanations of why first-generation associations between allelic markers
and traits such as disease resistance are often found and are usually
517. Early feeding
determines adult growth/reproduction trade-off
The influence of
juvenile and adult environments on life-history trajectories 2006. Taborsky, B. Proceedings of the Royal Society B: Biological Sciences
there is a trade-off between growth and reproductive traits, and if so, is
it the juvenile or the adult environment which determines the trade-off?
This is a highly relevant question for aquaculture. A simple but informative growth experiment designed to answer this
question was carried out on an occasional aquarium fish, the
mouth-breeding cichlid Simochromis pleurospilus. The abstract of the paper
cited here is exceptionally clear:
were raised either on a high-food or low-food diet. After maturation half
of them were switched to the opposite treatment, while the other half
remained unchanged. Adult growth was determined by current resource
availability, but key reproductive traits like reproductive rate and
offspring size were only influenced by juvenile growth conditions,
irrespective of the ration received as adults.
Moreover, the allocation
of resources to growth versus reproduction and to offspring number versus
size were shaped by juvenile rather than adult ecology [feed level]. These results indicate that early individual history
must be considered when analysing causes of life-history variation in
Wow. Juvenile feeding conditions determine adult growth/reproduction
tradeoffs. Of course, we don't know whether we can generalize these
observations. Has anyone done a similar experiment on shrimp? email@example.com