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.
News flash: a different and promising way to find adaptive MHC
Strong positive selection and habitat-specific amino acid substitution
patterns in Mhc from an estuarine fish under intense pollution stress.
2002. Cohen, S. Molecular Biology and Evolution 19:1870-1880.
MHC diversity is a very,
very hot topic in fisheries biology these days. The genetic diversity of
the major histocompatibility complex, which is the foundation of
vertebrate immune systems, appears to be driven by the diversity of
pathogens in the environment (see e.g. Jan 2003 #381). Fish may choose
their mates to optimize the MHC genotype of their offspring (Aug 2001 #221).
MHC has featured in
recent discussions of population
differentiation and the designation of evolutionarily significant units
for conservation (Dec 2001 #272, Mar 2002 #302).
Along with laboratory, field and theoretical studies of the
advantages of immune-system diversity per se, there have also been
demonstrations that specific pathogens can exert strong selection on
particular MHC alleles in fish (Dec 2002 #369). For all of the above
reasons MHC diversity considerations may become crucial (both practically
and politically) in the design of captive breeding and aquaculture
genetics programs (Dec 2002 #370). The
conclusions cited above are mostly based on population-level statistical
associations between survival and allele frequencies.
This clever study delves
deeper into the molecular structure of the MHC antigen-binding sites, and
could be a harbinger of more powerful ways to investigate and exploit MHC
diversity. One population of the study animal (Fundulus heteroclitus) lives
in an environment called the Hot Spot which has been grossly
polluted with PCBs and other contaminants for more than half a century.
This population has adapted to a concentration of contaminants which is
toxic to other Fundulus. It also carries high loads of parasites (helminths
and others) which are rare or absent in other Fundulus. In other words
fish in the Hot Spot are subject to strong and unusual antigenic
pressures. The other two populations live in more benign environments.
The conclusions of this work
are summarized in a visual
image which is both striking and instantly convincing -- a
3-dimensional structural model of the MHC Class IIB molecule with
population-specific amino acid substitutions shown as colored beads.
Substitutions which characterize different populations of Fundulus tend to be concentrated in different parts of the
antigen-binding region of the molecule. This image (Fig. 5) was reached
through a process which included identifying and cloning the MHC molecule
and sequencing a substantial number of individuals from different
The conclusion that the
MHC variation is driven by selection, not drift, are supported by careful
statistical analysis of MHC sequences from the various populations plus a parallel analysis of (presumably neutral) sequence variation in
mitochondrial DNA. "Whether Mhc population profile differences
represent the direct effects of chemical toxicants or indirect
parasite-mediated selection, the result is a composite habitat-specific
signature of strong selection and evolution affecting the genetic
repertoire of the major histocompatibility complex."
The first step in
applying this technique in other situations, e.g. searching for selectable
QTLs in an aquaculture broodstock, would seem to be finding a population
that is unusually well adapted to the targeted stress. firstname.lastname@example.org
A suggestion that hatchery supplementation should increase Ne of red drum
Spatial homogeneity and temporal
heterogeneity of red drum (Sciaenops ocellatus) microsatellites: effective
population sizes and management implications. 2002. Chapman, R. W., A. O. Ball and L. R. Mash.
Marine Biotechnology 4:589-603.
The red drum is an
important fish in the marine waters of the southern US, where it has
declined so much that fishing has been restricted and stock
supplementation is underway. Applying the temporal fluctuation method to
data on five microsatellite loci the authors estimate that effective
population size in the study site in South
Carolina may be in
the range 300 - 1000, which isn't very large. Therefore, they suggest that
since repeated augmentation should significantly increase the census size
it should also increase (not decrease) genetically effective population
number too. (See #391 below. See Feb 2002 #297 for effect of
supplementation on Ne.). email@example.com
Frankencarps are good fish
Effect of rainbow trout growth
hormone complementary DNA on body shape, carcass yield, and carcass
composition of F1 and F2 transgenic common carp (Cyprinus carpio). 2002. Dunham, R. A., N. Chatakondi, A. J.
Nichols, H. Kucuktas, C. Chen, D. A. Powers, J. D. Weete et al. Marine
"The altered body
shape of transgenic fish resulted in improved dressing percentage in the
F2 generation. The carcass composition of transgenic muscle had a lower
percentage of (P < 0.01) moisture and lipids and higher (P < 0.01)
percentage of protein in both generations. ... Also, the fatty acid profiles of both genotypes were minimally
altered." On the whole,
these transgenic carp not only grow faster than normal controls, they seem
to be a superior aquacultural product as well. firstname.lastname@example.org
Inbreeding does (often) remove deleterious genes from a population
Purging the genetic load: a
review of the experimental evidence. 2002. Crnokrak, P. and S. C. H. Barrett. Evolution 56:2347-2358.
This paper focuses on the question, "Does inbreeding purge
deleterious alleles from a population?" The answer is important both
for genetic conservation and for aquaculture, because if it is
"yes" a bold manager could decide to inbreed and select a
captive population so that inbreeding depression eventually becomes a
non-issue. The authors address the question through meta-analysis of
published paper on mammals, insects, mollusks and plants, but not fish. In a word, the answer does seem to be "yes".
Many of the analyzed populations eventually recovered some of the fitness lost in the early
generations of inbreeding (rebound), and hybrids between inbred
lines were often more fit than their ancestral populations. Less often,
they were more fit than non-inbred laboratory controls, which causes the
authors to suggest that adaptation to the laboratory (domestication)
can interfere with inbreeding experiments which are designed in certain
The meta-analysis is
highly significant, in the statistical sense, and supports the idea that
purging could be a useful management strategy in certain cases. "
firm predictions about the situations in which purging
is likely or the magnitude of fitness rebound possible when populations
are inbred remain difficult." The
meta-analysis also supports the idea that inbreeding depression is more
often the result of deleterious recessive alleles than of generalized
heterozygote advantage. For other discussions of purging and the cause of
inbreeding depression see Dec 2001 #265, Mar 2002 #307, Nov 2001 #259. email@example.com
Local genetic adaptation in salmon migratory returns
Genetic control over survival in
Pacific salmon (Oncorhynchus spp.): experimental evidence between and
within populations of
chinook salmon (O. tshawytscha).
2003. Unwin, M. J., M. T. Kinnison, N. C. Boustead and T. P. Quinn.
Canadian Journal of Fisheries and Aquatic Sciences 60:1-11.
The rapid evolution of life history traits in Chinook salmon which
were introduced to New Zealand in the early 1900s has already been noted
here (Oct 2000 #115). The authors of the earlier paper now report
that migrating salmon are relatively more successful in returning to the streams in which their ancestors evolved, compared to salmon whose
ancestors evolved in another stream. Furthermore, they find that there is
significant variation in return rate among paternal families. The authors take size and
non-additive genetic factors into account in their analysis of their
survival was positively correlated with weight at release, but there were
underlying genetic correlations unexplained by size. Taken together, these
results suggest considerable genetic influence over survival and return of
salmon and that population-specific adaptation can occur within 30
generations of establishment." "This rapid evolution is
particularly striking given the fact that the New Zealand rivers all
discharge into the South Pacific Ocean over a limited (~200 km) length of
coastline and that the major salmon-producing rivers (including those in
this study) have broadly similar physical characteristics." firstname.lastname@example.org
Inbreeding and selection generate 100% genetically all-male tilapia
Inheritance of sex in two ZZ
pseudofemale lines of tilapia Oreochromis aureus. 2003.
Damien, C. Mélard, M. C. Hoareau, Y. Bellemène, P. Bosc and J. F.
Baroiller. Aquaculture 218:131-140.
Males of the blue tilapia Oreochromis aureus have one kind of sex chromosome (ZZ), unlike O.
niloticus and the majority of fish farmers who have two (XY) sex
sex-reversal can produce ZZ blue tilapia which function as females and,
theoretically, should produce nothing but male offspring when mated with
ordinary ZZ males. Aquaculturists would like this because males grow faster and because all-male populations wouldn't
produce unproductive, resource-consuming offspring. Unfortunately the
actual proportion of males generated by ZZ x ZZ matings is usually much
less than 100%.
This interesting study
follows two populations of aureus through five generations of ZZ x ZZ
mating and family selection for high-male broods. One of the populations
was progressively and strongly inbred, the other was outbred. The
frequency of male offspring rose to nearly 100% in the inbred population
but did not increase significantly in the outbred population. The authors
suggest that this is because in the inbred population there
was much stronger selection on genes that are not on the sex chromosomes
but that nevertheless affect sex -- "autosomal" genes. Such
genes are known to complicate sex determination in O. niloticus,
another species in the same genus.
"The present study
also shows that it is possible to fix the male sex determining factors (Z
sex chromosome and genetic factors) in a line of
pseudofemales, producing a high percentage of male progeny in five
successive generations." "The genetic approach avoids the
hormonal sex-reversal treatment on a mass scale and the problem of
androgen residues in market-sized fish. The present study suggests that
the application of a genetic process to aquaculture requires strict
selection of both sexes (male and female) and not just of one sex
(super-male YY or pseudofemale ZZ)."
Of course the inbreeding
required in this approach is
likely to cause inbreeding depression of fitness and yield, a problem that will need to be solved by other
adjustments in the breed-development program or in the resulting
production program. email@example.com
Frankenpatents are delayed, but FrankenCubans are eating well
Transgenic salmon still out in
the cold in United States.
2003. Hoag, H. Nature 421:304.
vice-president of Aqua Bounty Farms, says that he doesn't expect the FDA
to approve the application
[for transgenic Atlantic salmon]
late 2004. The company plans to submit a second application, for
transgenic trout, in about a year's time. McGonigle says that the delay is
placing the company under financial strain. 'Money's an issue now,' he
says. 'We've been living on venture capital for years.' But a report
issued last week by the non-profit Pew Initiative on Food and
Biotechnology questioned the FDA's ability to regulate transgenic fish
properly. It says that the FDA lacks the expertise to evaluate
environmental risks. The report also calls for greater transparency and
public involvement in the review process."
researchers have been working with fast-growing transgenic carp since the
late 1980s, and
considering commercialization of tilapia that were first bred there in
1993. The Cuban researchers say it will be three years before they know
the regulatory fate of their tilapia. Mario Estrada, leader of the
aquatic-organism project at the Center for Genetic Engineering and
Biotechnology in Havana, says
that most of the food-safety studies are done, including an experiment in
which tilapia were eaten by volunteers."
The Pew report can be
downloaded from http://pewagbiotech.org/research/fish .
For more information
about the features of the Aqua Bounty salmon and how it was made see Jul
2000 #85, Sep 2000 #99. No e-mail address available.
Another large discrepancy between Ne and census number
Genetic effective size is three
orders of magnitude smaller than adult census size in an abundant,
estuarine-dependent marine fish (Sciaenops ocellatus). 2002.
Turner, T. F., J. P. Wares and J. R. Gold. Genetics 162:1329-1339.
This another recent
report of an extraordinarly
low population number in an important fish, red drum in the northern Gulf of
Mexico . Using
the temporal allelle-frequency-shift method the (short term) Ne was three
orders of magnitude lower than the estimated population size. Using a coalescent approach the estimated long-term Ne was
four orders of magnitude lower. The authors suggest that "The
extraordinarily low value of Ne/N appears to arise from high variance in
individual reproductive success and perhaps more importantly from variance
in productivity of critical spawning and nursery habitats located in
spatially discrete bays and estuaries throughout the northern Gulf".
And "Moreover, our study indicates that vertebrate populations with
enormous adult census numbers may still be at risk relative to decline and
extinction from genetic factors". (See #397, above. See Jan 2003 #385 for a 0.00001
A procedure for calculating population genetic statistics from AFLPs etc.
A Bayesian approach to inferring
population structure from dominant markers. 2002.
Holsinger, K. E., P. O. Lewis and D. K. Dey. Molecular Ecology
Developing primers for microsatellite markers in a new species
can be a lot of work, and for some organisms such as shrimp the combined
efforts of several labs have, to date, hardly provided enough published
Other sorts of genomic DNA markers, including amplified fragment length
polymorphisms (AFLPs) and RAPDs, dispense with the preliminary
species-specific DNA sequence analysis and are easier to find. Unfortunately such markers are dominant (homozygotes
carrying the marker cannot be distinguished from heterozygotes) and
standard techniques cannot easily be used to derive useful population
genetic statistics such as Fst. Or
if they are used for this purpose uncomfortable assumptions are needed.
The authors of this paper
describe a Bayesian method that "allows direct estimates of FST from
dominant markers ... we do not assume previous knowledge of the degree of
[or Hardy-Weinberg equilibrium]
....Simulations show that samples from even a relatively small number of
loci and populations produce reliable estimates of FST. Moreover, some
information about the degree of within-population inbreeding (FIS) is
available from data sets with a large number of loci and
populations." firstname.lastname@example.org .
How to estimate quantitative genetic parameters after all the runts have
Estimation of additive genetic
variance components in aquaculture populations selectively pedigreed by
2003. Li, X., C. Field and R. W. Doyle. Biometrical Journal 45:61-72.
"A method to
estimate genetic variance components in populations partially pedigreed by
DNA fingerprinting is presented. The focus is on aquaculture, where ...
the individuals available for measurement will often be selected, i.e.
will come from the upper tail of a size-at-age distribution, or the lower
tail of an age-at-maturity distribution etc. Selection typically occurs by
size grading during grow-out
[plus size-selective mortality including cannibalism]
choice of superior fish as broodstock. The method presented in this paper
enables us to estimate genetic variance components when only a small
proportion of individuals, those with extreme phenotypes, have been
identified by DNA fingerprinting....
of variance or maximum likelihood estimation cannot be used when only the
extreme progeny have been pedigreed because of the biased nature of the
estimates. In our model-based procedure a full robust likelihood function
is defined, in which the missing information about non-extreme progeny has
been taken into account." email@example.com
Captive breeding probably saved a small population from extinction
Population on the verge of a
mutational meltdown? Fitness costs of genetic load for an amphibian in the
2003. Rowe, G. and T. J. C. Beebee. Evolution 57:177-181.
Norwegian graylings have been shown to adapt rapidly to a new
environment despite severe bottlenecking (Dec 2002 #364). But in the dice snake
serial bottlenecking produced a fitness decline (Jan 2003 #376). The
authors of this report studied the fitness of a small population of toads
(Bufo calamita) at the extreme of the natural range, relative to an
outbred population in the same environment. Both populations were held in
semi-natural field enclosures. How has the balance between local
adaptative improvement and decline due to drift+inbreeding worked itself out in this case?
If the isolated,
bottlenecked toads ever achieved any special adaptation to their local
environment they must have lost it before these experimenters came along.
"Key larval fitness attributes in B. calamita, notably growth rate
and metamorph production, were substantially higher in the large
outbreeding population (Ainsdale) than in the small and isolated one (Saltfleetby)."
"The Saltfleetby toad population was both larger and less isolated
(because neighbouring populations have subsequently become extinct) during
the nineteenth century than is the case today.
"The low fitness of
Saltfleetby relative to Ainsdale toads at the present time may be best
explained by an increased genetic load at Saltfleetby, reflected in the
higher levels of average homozygosity at microsatellite loci in the
smaller population." The small population also exhibited reduced
genetic (microsatellite) variability.
These observations seem
to bear on the vexed question whether captive breeding (e.g. of salmon) is
a bad idea under all circumstances and whether money spent on live gene banks
would always be better spent on habitat restoration.
"Two other small
populations of this toad have become extinct in
past 20 years without obvious cause and despite substantial habitat
management. …It is very unlikely that the Saltfleetby population would
have survived without the extensive captive rearing and release of
toadlets that has continued for more than 20 years. Extensive habitat
management has failed to improve this population’s viability. Our
results confirm that extinction is a far more likely outcome of population
isolation than the emergence of new locally adapted forms." firstname.lastname@example.org
Local adaptation despite prolonged planktonic dispersal
Genetic evidence for local
retention of pelagic larvae in a Caribbean reef fish. 2003. Taylor, M. S. and M. E. Hellberg.
It used to be assumed
that a long stay in the plankton would ensure that populations disperse
widely, so adaptation to particular, local environments would have to
begin all over again every generation. There is plenty of genetic evidence
for this and a good life-history theory to go with it (elm-oyster model, sweepstakes model; see Nov 2001 #259). However, there is now good
and quite surprising evidence that planktonic larvae of some marine
species (perhaps a lot of species) somehow avoid being spread all over the
ocean and can maintain complicated evolutionary geographies. For a recent
example see Jan 2003 #375.
The authors of this paper
looked at mitochondrial and other genetic markers in the and
Bahamian cleaner goby Elacatinus evelynae. The planktonic
stage lasts about three weeks. There is strong genetic differentiation among populations in different
islands and colour patterns also differ on a regional basis, suggesting that the animals which host these cleaner fish
might be exerting selection for particular, local colour patterns.
"These results suggest that marine populations can remain
demographically closed for thousands of generations despite extended
larval duration, and that recognition cues such as color may promote
speciation when geographic barriers are transient or weak."
Palumbi has commented on this paper in the same issue of Science. mtayL22@lsu.edu ; email@example.com .
Detecting & correcting pedigree and marker data problems
GENCHECK: A program for
consistency checking and derivation of genotypes at co-dominant and
2002. Bennewitz, J., N. Reinsch and E. Kalm. Journal of Animal Breeding
and Genetics 119:350-360.
developed to examine genotyping results of diploid organisms for
consistency with the Mendelian laws of inheritance. It can be used to
analyse data from co-dominant and dominant loci and large scale pedigrees
with many overlapping generations as they are common in animal breeding.
...The data from individuals, whose genotyping results show a Mendelian
segregation error, are written to an output file. ... Additionally, the
program derives, if possible, the genotypes of untyped individuals or of
individuals, whose genotyping results were assumed to cause a Mendelian
segregation error, using information from the parents and/or the
offspring. ... The program is written in Fortran 90 and available from the