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.
516. The proper way to measure mortality in
Genetic parameters and accuracy of selection for
resistance to White Spot Syndrome Virus (WSSV) in Penaeus (Litopenaeus)
vannamei using different statistical models. 2006. Gitterle, T., J. Ødegård, B. Gjerde,
M. Rye and R. Salte. Aquaculture 251:210-218.
This useful paper from Akvaforsk (in collaboration with CENIACUA, Centro de
Investigaciones para la Acuicultura en Colombia) compares the
effectiveness of various ways of measuring mortality in disease challenge
tests. The Cox model, which uses an age-at-death variable, worked best. In this particular
identities of newly dead and moribund animals were recorded every hour
during the test. (This much data is nice to have but may be overkill in a
on these results we suggest selection programs for white spot resistance
should be based on ... models taking time to death into account with
proper model of the mortality pattern of the test population ..., rather
than the models that define survival as a binary trait at 50%
No one should disagree with this conclusion. Standard challenge test methodologies,
in which each family receives only one score (e.g. % survival) are
profoundly unsatisfactory for genetic analysis or practical selection in
aquaculture. Too much information is thrown away in each test. Attempts to
add information by increasing the number of families and replicates/family
can be horribly expensive and
generally add new sources of variation which are either ignored (defeating
the purpose of the expansion) or necessitate additional parameter
estimates (ditto). firstname.lastname@example.org
515. measure of quantitative trait
effects of dominance, regular inbreeding and sampling design on QST, an
estimator of population differentiation for quantitative traits. 2006.
Goude, J. and L. Büchi. Genetics 172:1337-1347.
years ago a meta-analysis of 18 published cases found that
populations usually differ more in distributions of quantitative traits,
measured by QST, than in frequencies of neutral markers, measured by FST
(Jan 2002 #281). QST and FST are analogous measures of variance among and within
populations for these two types of traits.
That paper concluded that
natural selection is the predominant force driving populations
toward different mean values of quantitative traits. That is, mean
quantitative genetic differences in growth, appearance, physiology and
behaviour are due more to selection than drift. An important conclusion.
that if both types of traits are selectively neutral the prediction is QST=FST,
if populations are selected in different directions there is more
quantitative divergence so QST > FST, and if selection tends to bring
populations towards a common optimum then QST<FST.)
paper cited here is an analytical and simulation study of the influence of
non-additive effects such as dominance and inbreeding on the ratio of GST
to FST. "Provided that estimates of QST are derived from individuals
originating from many populations, we conclude that the pattern QST >
FST, and hence the inference of directional selection for different local
optima, is robust to the effect of nonadditive gene actions." Good. email@example.com
514. Domesticated O. niloticus not as good
as wild ones
On-farm and on-station comparison of wild and
domesticated Cameroonian populations of Oreochromis niloticus. 2004. Brummett, R. E., D. E. Angoni and V. Pouomogne. Aquaculture
Grand-offspring of a wild population out-grew and out-produced
a domesticated population in
this trial, after at least 25 years of domestication. The
difference was considerable. Why does domestication tend to cause cultured tilapia to deteriorate everywhere in the world unless
carefully designed selection programs are maintained?
The authors of this
paper ascribe their particular results to the regional management history
of tilapia, and they are doubtless correct. But informally managed salmonids and carp don't deteriorate,
nor do penaeid shrimp unless they're seriously inbred. Why do tilapia go
bad so consistently?
My guess is that it has to do with the tendency of Oreochromis to
"stunt" -- reproduce young and small -- as part of its normal
life history strategy under some social and environmental conditions,
particularly crowding. Careless domestication selects for a lower stunting threshold.
Just a guess. firstname.lastname@example.org
513. Damage to DNA
study ancient populations
Assessing the fidelity of ancient DNA sequences
amplified from nuclear genes. 2006. Binladen, J. and others. Genetics 172:733-741.
This study takes a detailed look at changes in nuclear DNA
which take place postmortem and which may affect genetic inferences about
long-ago migrations and hybridizations (e.g. Jan 2003 #380, Jan-Feb 2004
#461 & #464).
comparing clone sequences from 23 fossil specimens ... we demonstrate the
presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting
in insertion of erroneous bases during amplification." The samples
studied (woolly mammoths, rhinoceroses etc.) were much older than those
used in the papers cited above, but changes caused by microorganisms,
cellular nucleases and non-enzymatic oxidation and hydrolysis are
presumably the same.
The authors also make the useful point that museums
and herbariums are not good storage environments for DNA, compared with
deserts and permafrost. email@example.com
512. Walk-back selection with improved use of kinship
A combination of walk-back and optimum contribution
selection in fish: a simulation study. 2005. Sonesson, A. K. Genetics Selection
selection is a procedure for use in simple aquaculture set-ups
where many families are reared together in one tank or pond. The best
(e.g. largest) animal is selected as a breeder and DNA markers are used to
identify its family. The second-largest animal is then identified and, if
it comes from a different family it too is selected; if it belongs to the
same family and sex as the first it is rejected. The third, fourth ... best
animals are identified and selected if they are from different families,
"walking back" from the right-hand end of the size distribution
towards the mean.
Walk-back stops when enough
pairs have been selected to
attain the desired broodstock population number. Walk-back is a type of
within-family selection adapted to the high fecundity of aquacultural
species and the high cost of rearing individual families.
This paper simulates a combination of walk-back and "optimum
contribution" selection (see Dec 2001 #270, also Apr 2003 #473, Aug
2002 #335) which makes a more sophisticated use of kinship than merely
discarding duplicates from the same family. The paper confirms that high
rates of genetic gain and low inbreeding can be attained relatively
easily, i.e. by genotyping a few hundred animals, not thousands. Anna.Sonesson@akvaforsk.no
there be many management units or one?
Reconciling nuclear microsatellite and mitochondrial
marker estimates of population structure: breeding population structure of
Chesapeake Bay striped bass (Morone saxatilis).
2005. Brown, K. M., G. A. Baltazar and M. B. Hamilton. Heredity
about the sizes and histories of populations based on nuclear markers
(e.g. microsatellites) commonly differ from inferences based on organelle
markers (e.g. mitochondrial D-loop sequence). An example is the striped
bass population of Chesapeake Bay, where it is uncertain whether
sub-populations inhabiting the in-flowing rivers should be considered
distinct management units.
This paper reconciles the
contradictory conclusions from previous protein, microsatellite and mtDNA
studies. "Reanalysis of Chesapeake Bay striped bass mtDNA data from
two previous studies estimated population differentiation between =-0.002
and 0.160, values generally similar to mtDNA population differentiation
predicted from microsatellite RST after adjusting for reduced effective
population size and uniparental inheritance in organelle genomes."
The bottom line: It's a panmictic population and one management unit. See
Jan-Feb 2004 #464 re metapopulation. firstname.lastname@example.org
510. Estimating genetic correlations involving survival
A bivariate quantitative genetic model for a linear
Gaussian trait and a survival trait. 2006. Damgaard, L. H. and I. R. Korsgaard.
Genetics Selection Evolution 38:45-64.
now -- believe it or not -- there has been no correct way to use modern
REML/BLUP procedures when jointly analysing bivariate genetic correlations
(or selection indices) involving yes-or-no survival plus a continuous,
quantitative trait like growth.
The approximation everyone
falls back on wastes
information (e.g. correlations of univariate estimates from Ducrocq's and
Sölkner's "Survival Kit", Jul-Aug 2002 #343). The usual approximation
is also biased by environmental effects, which may be especially severe in
aquaculture when growth is density-dependent.
authors of this technical paper describe a Gibbs sampler for joint Bayesian
analysis of a normally-distributed linear trait and a survival trait,
which are genetically and environmentally correlated. "The bivariate
model allows for a more accurate genetic evaluation of animals ... owing
to the shared information between traits. ... The results from these [simulation] analyses
indicated clearly that the approximative method can be very
imply that practical implementation of their procedure should be
relatively straight-forward but do not as yet offer us a program.
Note that if
time-to-death, a continuous variable, is measured (see #516) the correlation
difficulty mentioned here disappears. email@example.com
509. The P. monodon map continues to be filled in
Development of polymorphic expressed sequence
tag-derived microsatellites for the extension of the genetic linkage map
of the black tiger shrimp (Penaeus monodon). 2006. Maneeruttanarungroj, C. and others.
Animal Genetics 37:363-368.
total of 997 unique microsatellite-containing expressed sequence tags (ESTs)
were identified... .an average number of alleles of 12.6 and an average [marker] polymorphic information content of 0.723... .The current P. monodon male
and female linkage maps have 47 and 36 linkage groups respectively with
coverage across half the P. monodon genome." firstname.lastname@example.org
508. Early life history is not changed by fishing
Harvest selection, genetic
correlations, and evolutionary changes in recruitment: one less thing to
worry about? 2005. Munch, S. B., M. R. Walsh and D. O. Conover.
Canadian Journal Fisheries and Aquatic Sciences 62:802-810.
research group has been "fishing" -- harvesting -- an
experimental population of the
Atlantic silversides (Menidia menidia) for about 25 years and interesting
results continue to be published. They find significant realized genetic
correlation between adult size (the target of size-selective fishing) and
egg diameter, larval viability and several juvenile and adult size
variables which are known to affect one or another component of
Nevertheless, "In contrast with studies of harvest
selection on adult characteristics, we find the response of characters in
the early life history to be relatively slow and that impacts on
recruitment, if any, are likely to be driven by selective changes in
fecundity." The low-impact prediction derives from the sensitivity of
their model of recruitment to the magnitude of the predicted correlated
evolution of the early life history variables. See Jul-Aug 2003 #345. email@example.com
507. Possible inbreeding and outbreeding
depression in bluegill sunfish
Stabilizing selection on genomic divergence in a wild
fish population. 2004. Neff, B. D. Proceedings National Acad. Sciences USA 101:2381-2385.
managed populations it is frequently recommended to select and mate
animals with low genetic relatedness (i.e. which are not closely
associated with other animals in the pedigree of the population) so as to
minimize inbreeding depression (see #512 and Jan 2002 #283, Jul-Aug 2002 #335, Mar-Apr
2004 #473). In doing this, though, one risks elimination of special
adaptations or locally-adapted complexes of genes, thus causing
outbreeding depression [e.g. Apr-May 2003 #400].
In aquaculture, where the aim is to adapt a domestic stock to an
artificial environment, outbreeding depression is not a big worry
(except perhaps in choosing a founders for the stock, where the issue
might better be labeled pre-adaptation). But when the aim is genetic
conservation of endangered wild populations outbreeding is a
concern and evidence for it is avidly sought.
microsatellite markers are used to estimate whether naturally mated
parents of wild bluegill sunfish (Lepomis macrochirus) are relatively
closely related (potential inbreeders) or distantly related (potential
outbreeders). The results seem to imply that mates chose each other to
avoid both inbreeding and outbreeding, i.e. there was stabilizing
selection for intermediate relatedness.
Fluctuating asymmetry, possibly
and inverse measure of fitness [Jul-Aug
higher at both extremes of parental
relatedness. Reproductive success, a direct component of fitness, was
higher in the middle. No effect on condition factor and parasite load could be detected. firstname.lastname@example.org
506. Thai TSV more related to Asian than American
Taura syndrome virus (TSV) in Thailand and its
relationship to TSV in China and the Americas. 2005.
Nielsen, L., W. Sang-oum, S. Cheevadhanarak and T. W. Flegel. Diseases of
Aquatic Organisms 63:101-106.
has more-or-less banned importation of Penaeus vannamei and P. monodon
since February 2003 owing to fear of importing Taura syndrome virus (TSV).
The TSV disease is present in Thailand, though, and in the interest of
assigning blame we want to know where it comes from. In this study
"Comparison [of viral
coat protein gene VP1] revealed that the Thai, Burmese and Chinese TSV types
formed a clade distinct from a clade of TSV types from the Americas." email@example.com
505. Wild catfish not genetically harmed by aquaculture
Comparison of domestic and wild channel catfish (Ictalurus
punctatus) populations provides no evidence for genetic impact. 2006.
Simmons, M., K. Mickett, H. Kucuktas, P. Li, R. Dunham and Z. Liu.
study is based on AFLP polymorphisms and straightforward Fst and distance
calculations. There is a lot of catfish cultivation in the southern USA
and a lot of wild catfish grow there as well. Escapes must be common but
the genetic impact seems to be small.
"The domestic populations were
all related to one another, forming a single branch in the phylogenetic
analysis, while all but the Tennessee River populations of many wild
populations were more related to one another than to domestic populations.
Genetic identities of wild fish from proximal and distal sites were
similar, while both wild populations differed from the nearby domestic
catfish populations, providing no molecular genetic evidence for apparent
impact of domestic catfish on wild populations." firstname.lastname@example.org