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.
Tilapia mass-spawning increases the
rate of inbreeding
Mating systems and male reproductive success in Nile
tilapia (Oreochromis niloticus) in breeding hapas: A microsatellite
analysis. 2006. Fessehaye, Y., Z. El-bialy, M. A. Rezk, R. Crooijmans, H. Bovenhuis
and H. Komen. Aquaculture 256:148-158.
Mass spawning in cages (hapas)
is a common practice in tilapia aquaculture. Some males and females breed
much more than
others, which increases inbreeding. How bad is
The PAPA program (Nov-Dec 2003 #446) was used with 11 microsatellite
parental identification in this study of tilapia morality in hapas. "Multiple paternity was detected in 70% of
the broods, with up to 4 males fertilizing a single clutch. Multiple
maternity was also detected in over 30% of the clutches analyzed. There
was a very high variance in male reproductive success, with one third of
males siring more than 70% of the offspring. Male condition factor had a
significant effect on reproductive success with larger males siring a
large proportion of offspring."
The rate of
inbreeding was about twice what it would have been under optimal
evolution of genes and gene
Parallelism in gene transcription among sympatric lake
whitefish (Coregonus clupeaformis Mitchill) ecotypes.
2006. Derome, N., P. Duchesne and L. Bernatchez. Molecular Ecology
Two ecotypes of whitefish,
benthic and limnetic,
which have diverged in their
behaviour, energy metabolism and morphology are found together in
countless Canadian lakes.
Despite the genetic isolation
of the pairs a large
number of their genes have evolved parallel
changes in sequence and/or expression profiles in different lakes.
In particular, "Fifty-one genes (4.3%) showed parallel
differential expression between lakes, among which 35 were expressed in
opposite directions. Sixteen genes (1.35%) showed true parallelism of
transcription, which mainly belonged to energetic metabolism and
regulation of muscle contraction functional groups. Variance in expression
was significantly reduced for these genes compared to those not showing
directionality in parallelism of expression."
The authors note that
the growing evidence that parallel phenotypic evolution also involves
parallelism at both the genotypic and regulatory level, which may at least
partly be associated with genetic constraints."
the authors remind us, gene expression is a quantitative trait, so the
lower variance of selected traits, relative to unselected traits accords with Fisher's fundamental
with Nov-Dec 2003 #441 in which twenty thousand generations of
experimental evolution of two bacterial populations also produced many
parallel sequence and transcription changes, again with constraints, or at
least contingencies of the "if mutation a then mutation b,
if not a then c" variety.
is an excellent model for work with similar objectives. Ttranscription analysis employed a 3557 cDNA gene microarray developed for
the Genomic Research on Atlantic Salmon Project (GRASP; Genome Research 14, 478–490, 2004). The statistical analysis, although described
rather briefly, is well referenced and ultimately rests its case for
significance on a type of randomization test. email@example.com
502. Venezuelan vannamei
has improved under selection
Mass selection and inbreeding effects on a cultivated
strain of Penaeus (Litopenaeus) vannamei in Venezuela. 2005. De Donato, M., R. Manrique, R. Ramirez, L. Mayer and C. Howell.
reproductive stock of the farm was established from three different
populations mixed in successive generations (Mexico first generation,
Panama second generation, and Colombia third generation)." Eleven
generations of mass selection had been completed at the time of writing.
Growth, survival and FCR all improved substantially over this time. IHHNV
(a viral disease which produces deformities) caused trouble in the early
generations but disappeared later on. The authors attribute this to a
selective purging of genes which produced symptoms of inbreeding
depression in the founding stocks. For an explanation of purging see Feb-Mar 2003 #395. firstname.lastname@example.org
501. Extreme selection for MHC diversity
High MHC diversity maintained by balancing
selection in an otherwise genetically monomorphic mammal. 2004.
Aguilar, A., G. Roemer, S. Debenham, M. Binns, D. Garcelon and R. K.
Wayne. Proceedings National Academy of Science (US) 101:3490-3494.
San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the
most monomorphic sexually reproducing animal population yet reported and
has no variation in hypervariable genetic markers." This is extreme -- no marker variation at all, even in microsatellites and
multilocus fingerprints? Yet the foxes do have extremely high levels of
MHC variation, presumably maintained by balancing selection.
This shows how important MHC diversity can be:
the authors estimate that a selection intensity of 0.5 is required to
maintain diversity through the severe bottlenecking which is implied by
the absence of neutral marker variation. There has to have been a
bottleneck severe enough to eliminate microsatellite diversity, and recent
enough so that new diversity has not arisen through mutation. This
selection is enormously strong compared to other selection intensities
which have been estimated in nature. A correlation between MHC diversity
and individual fitness components is often observed, but is also often
much weaker than one might expect.
The authors observe that since MHC
diversity is uncoupled from microsatellite diversity in this population,
microsatellites may not be a good surrogate measure of what is worth
preserving in protected populations. They conclude with the comment
"Preservation of a diverse array of fitness-related genes, along with
neutral variation, might be the key to the long-term survival of
endangered populations." See Feb 2002 #286. email@example.com
500. Candidate genes not a good way to look for QTLs?
Evaluation of candidate genes in the absence of
positional information: a poor bet on a blind dog! 2005. Aguirre-Hernández, J. and S. D.R. Journal of Heredity 96:475-484.
This paper about dogs evaluates a large number of candidate gene studies on
retinal disease, of which only 3.4% found a causal QTL (mutation).
"On the other hand, five linkage analysis studies have been done on
retinal diseases, resulting in three identified mutations and two mapped
A lot more
is known about dogs than about any aquacultural species, so we might take
this as a useful "heads up". Note #496 where one candidate gene out of many was found to be
499. Positive correlation between growth and survival
Genetic (co)variation in harvest body weight and
survival in Penaeus (Litopenaeus) vannamei under standard commercial
conditions. 2005. Gitterle, T., M. Rye, R. Salte, J. Cock, H. Johansen, C. Lozano,
J. A. Suárez et al. Aquaculture 243:83-92.
this study, conducted in tanks and ponds in Colombia, heritability of
growth was moderate (around 0.2) and heritability of survival was low (<=0.1).
The authors report a positive genetic correlation of around 0.4 between growth and survival.
Their conclusion is good news for aquaculture: "... selecting for
growth will cause a positive correlated response in overall survival. The
genetic correlations between body weights and pond/tank survival in
different grow-out environments were high, demonstrating low genotype by
farm interaction (GXE) for both traits."
Aquaculture 246:139-149. 2005
is a paper by the same authors on the same population, in which resistance to
WSSV had low heritability but nevertheless is negatively correlated with harvest weight. firstname.lastname@example.org
determination in O. aureus
Two unlinked loci controlling the sex of blue tilapia (Oreochromis
aureus). 2004. Lee, B.-Y., G. Hulata and T. D. Kocher. Heredity
of the two proposed sex-controlling genes is a dominant male repressor and the other is a dominant male determiner. Markers closely linked
to the genes "have immediate utility for studying the strength of
different sex chromosome alleles, and for identifying broodstock carrying
copies of the W [male
The W-markers correctly predict the phenotypic sex of sex of almost all
males and 85% of the females in the one family used in the linkage
497. Finding hidden genetic barriers in the ocean .
Marine landscapes and population genetic
structure of herring (Clupea harengus L.) in the Baltic Sea. 2005.
Jørgensen, H. B. H., M. M. Hansen, D. Bekkevold, D. E. Ruzzante and
V. Loeschcke. Molecular Ecology 14:3219-3234.
most interesting aspect of this study is the discovery of "two
zones of lowered gene flow[among herring spawning groups]. These
zones were concordant with the separation of the Baltic Sea into major
basins, with environmental gradients and with differences in migration
The analysis features a fascinating
procedure and program for identifying genetic "barriers" which
has been developed by Manni, Guérard & Heyer (Human Biology 76(2).
2004. 173–190. http://www.mnhn.fr/mnhn/ecoanthropologie/software/barrier.html).
The BARRIERS program implements a computational geometry
identifying genetic discontinuities within a geographical coordinate
system, that is, for finding locations where genetic distances -- or any
other metric, or function of metrics for that matter -- show an abrupt
The authors of the herring paper
found that the Manni, Guérard
& Heyer algorithm provides insights into geographical structuring
which go well beyond those provided by multidimensional scaling, Mantel's
procedure and the other more familiar procedures they tried. email@example.com
496. A large-effect QTL for spawning time in trout
The candidate gene, Clock, localizes to a
strong spawning time quantitative trait locus region in rainbow trout. 2006.
Leder, E. H., R. G. Danzmann and M. M. Ferguson. Journal of Heredity
has been known for some time that the optic tectum and the pretectal area
of the rainbow trout are major sites of integration of the melatonin
signal, express the clock gene, and may act as biological clocks to
influence behavioral and endocrine responses in trout (Mazurais et al. J.
Comp. Neurol. 422:612-620, 2000).
this paper, "Interval mapping was used to identify associations
between genetic markers and spawning date effects. ...a strong QTL region
was identified in both female and male parents on linkage group RT-8 that
explained 20% and 50% of trait [spawning time] variance, respectively. The
Clock gene mapped to this region."
Note that there were 775 markers
available for the study and several traits and several candidate genes
were analysed, of which only the Clock association was noteworthy. See
495. The Kona line of vannamei is indeed susceptible to
Comparison of four Taura syndrome virus (TSV) isolates
in oral challenge studies with Litopenaeus vannamei unselected or selected
for resistance to TSV. 2006. Srisuvan, T., B. L. Noble, P. J. Schofield and D. V. Lightner.
Diseases of Aquatic Organisms 71:1-10.
well-known Hawaiian shrimp (vannamei) populations were compared: a specific
pathogen free, Taura syndrome resistant commercial line from High-Health
Aquaculture (TSR), and the Kona line from the Oceanic Institute, a line which is
known to be rather susceptible to this disease and which is often used as
an experimental control or "sentinel" line.
The lab exposed the
test animals to a variety of challenge procedures and analytical
procedures. Also, four different strains of virus were used.
The Kona shrimp had lower survival rates when challenged with all four
strains. Only one of the viral strains caused lesions in TSR but all 4 did
so in Kona. Viral load for three of the four strains was higher in Kona
than in the TSR line. firstname.lastname@example.org
494. Analysis of economic/genetic tradeoffs in breed
Optimum allocation of conservation funds and choice of
conservation programs for a set of African cattle breeds. 2006. Reist-Marti, S. B., A. Abdulai and H. Simianer. Genetics Selection
authors have examined the choice of breeds according to their endangerment
or their endangerment and contribution to diversity [Nov-Dec 2002 #371, Apr-May 2003 #410] . In other
studies the cost of different conservation programs and their effects have
been analyzed. Yet, research on how to use the limited funds on the breeds
most efficiently, i.e. with the highest conserved diversity possible is
it is. The procedure described
in this paper divides up hypothetical budgets, discounted over
50 years, among 50 African cattle and several conservations objectives
including risk of extinction, global genetic diversity, economically
important breed-specific traits etc.
"Pure in situ conservation [giving responsibility to local breeders] was more
efficient than cryoconservation or combined in situ and cryoconservation."
various hypothetical conservation procedures are quite specific and will
be conceptually familiar to practical geneticists. For instance, the pure
in situ procedure, "consists of a circular mating scheme, where sires
rotate between 10/30 cow groups. Each group consists of five cows and one
sire. The cows are owned by farmers and the sires belong to the program.
The sires and cows are replaced by one of their offspring every fifth year
when the rotation of sires takes place."
The procedure takes not only
the genetic considerations into account but also the economic status of
the farmers and countries concerned, and even foreign exchange rates, in
what appears to me (a non-economist) as a sophisticated model.
The approach is described with a generality which will make it interesting to
many sorts of aquaculture and breed conservation schemes. email@example.com
493. Reduced selection doesn't result in loss of fitness
Relaxation of selection with equalization of parental contributions in conservation programs: an experimental test with
Drosophila melanogaster. 2006. Rodríguez-Ramilo, S. T., P. Morán and A. Caballero. Genetics
is a well known precept (but perhaps less well followed than known) that
to maximize the effective population size of an aquacultural or captive
broodstock one should equalize the reproductive output of the parents.
That is, make sure all males and all female breeders have the same number
of offspring. There are other schemes, especially those that use
pedigree information to minimize the mean kinship of the breeders (Apr
2004 #473, Feb 2004#455, Nov 2001 #261). The objective of all such schemes
is to reduce inbreeding and genetic drift to their lowest feasible level.
problem is, if you artificially force breeders to have equal family sizes
you are eliminating a lot of individual selection on, among other things,
fecundity, mating behaviour, mate choice, early-stage survival and so on,
plus, of course, selection between families. Does the relaxation of
selection caused by enforced reproductive equality have deleterious
long-term effects on fitness?
It is a worry to take seriously, especially
in conservation breeding where the ultimate objective is to re-establish a
experiment on fruit flies, in which selection was relaxed for 38
generations, did not result in a loss of fitness which was
significantly greater than losses in the control. (Control lines enjoyed
free mating and natural family sizes, equal reproductive contribution was enforced on the relaxed
The main objective of equalization was achieved,
retained higher gene diversity and allelic richness for four
microsatellite markers and a higher heritability for sternopleural bristle
The feared excessive loss of fitness did not happen.
"Our results, therefore, provide no evidence to suggest that
equalization of family sizes entails a disadvantage on the reproductive
capacity of conserved populations in comparison with no management
procedures, even after long periods of captivity."
Mar 2002 #300 for an experiment with similar objectives which differed
both in its design and its outcome. firstname.lastname@example.org