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.
440. Should you select late-maturing male trout?
Selection against early maturity
in large rainbow trout Oncorhynchus mykiss: the quantitative genetics of
sexual dimorphism and genotype-by-environment interactions. 2003. Kause, A., O. Ritola, T. Paananen, E. Mäntysaari and U. Eskelinen.
salmon and trout are a problem for aquaculture because the fish are
physically and morally unappealing and their growth
slow. Some males mature early and some mature late, but almost all females
This interesting paper
looks at the heritabilities of growth and maturation in both sexes and the
genetic correlation between traits and sexes. The practical motivation is
to see if one can change the sexual dimorphism by selection to develop a strain in which all the males mature late but the maturation of
females is unchanged. The answer appears to be no. Age-at maturation is
more-or-less the same trait in both sexes, judging by the strong genetic
correlation between the males and females for both maturation and weight.
This is interesting in the light of a report that markers for maturation
may differ in male and female rainbow trout (Jan 2001 #160). The
heritability of both traits is sufficiently high, though, that selection for
late maturation of both sexes should work if performed on either sex.
Rapid growth is
genetically correlated with early maturation in both sexes, but this
unfortunate correlation is probably not strong enough to cause major
problems in artificial selection for commercial performance. In fact there
are reports that age-at-maturation evolves rapidly under natural selection
(Oct 2000 #115, May 2002 #315). "Extensive
data set including individuals in five generations measured in brackish
and fresh water [in
Finland] in a
split-family design was utilised to estimate the genetic parameters." firstname.lastname@example.org
439. You need pedigree data to
manage a small population
Pedigree and marker information
requirements to monitor genetic variability. 2003. Baumung, R. and J. Sölkner. Genetics Selection
You shouldn't leave
matings to chance if you are managing a small population. The optimal choice of breeders and
mating strategy depend
critically on inbreeding coefficients and the genetic
relatedness of potential mates (Aug 2001 #212, Nov 2001 #261, Aug 2002
#335). But how does one get this kind of information? Either directly from
pedigree records or indirectly from genetic markers (e.g. SNPs, AFLPs,
The effectiveness of the
direct and indirect procedures are compared in this very useful simulation study. In a
number of different mating schemes, including random mating, sib-avoidance
etc., markers did less well than pedigrees at estimating the principal
quantity of interest, which is the proportion of alleles identical by
descent (inbreeding defined as autozygosity). When pedigree records are
used, the correlation between true and estimated autozygosity was always
>0.6, even when only the most recent couple of generations are included.
"Therefore it seems to be possible to identify the most autozygous
animals assuming parents and grandparents are known." By the
standards of aquaculture and fisheries this is
probably pretty good. It is also useful to learn that "taking more
than five generations of a correct pedigree into account leads only to a
marginal increase of the correlation of pedigree inbreeding coefficients
By contrast, the performance of marker-based estimates was disappointing. "The simulations show that even
pedigrees of low quality allow the identification of the most autozygous
animals in a random mating population. [However] Measures
based on codominant marker loci lead to comparable results only when more
than 100 (better 200) microsatellite loci are typed." This agrees
with the disappointing conclusion about marker-based kinship estimation
cited in Dec 2002 #362. email@example.com
438. Frankensalmon are motivated to feed
Oxygen uptake of growth hormone
transgenic coho salmon during starvation and feeding. 2003. Leggatt, R. A., R. H. Devlin, A. P.
Farrell and D. J. Randall. Journal of Fish Biology 62:1053-1066.
carrying all-salmon growth hormone gene assembly ate more and grew faster
than control salmon in this experiment, and they also used oxygen at a
higher rate. "Differences in oxygen uptake in growth hormone
transgenic coho salmon and non-transgenic fish appear to be due to the
effects of feeding, acclimation and activity level, and not to a
difference in basal metabolism." The authors believe that the increased
oxygen uptake is also due in part to increased food conversion efficiency.
"While in the holding tanks, the transgenic and control fish
displayed very different behaviours. The control fish tended to stay near
the bottom corners of the tank, but became active when disturbed. The
transgenic fish tended stay near the surface of the water and were active
most of the time." The frankensalmon also acclimated more quickly to
the respirometer. The authors explain this by saying that the extra growth
hormone gene motivates the fish more towards feeding and less towards
predator avoidance. See
Jul 2000 #81 and Feb 2001 #174. firstname.lastname@example.org
437. Vannamei marker sequences
High frequency and large number
of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus)
vannamei [Crustacea:Decapoda] . 2003. Meehan, D., Z. Xu, G. Zuniga and A. Alcivar-Warren.
Marine Biotechnology 5:311-330.
The authors have
developed dozens of useful microsatellite markers and here they very
helpfully publish the forward and reverse primers together with some comments on
the spanned repeat sequences (e.g. "perfect", "imperfect"),
the number of alleles in the sample they studied, etc. email@example.com
436. Animals grow slower in a
genetically impoverished population
The relationship between genetic
variability and growth rate among populations of the pocket gopher, Thomomys
bottae. 2003. Hildner, K. K., M.
E. Soulé, M.-S. Min and D. R. Foran. Conservation Genetics 4:233-240.
An important question in aquaculture and genetic conservation is whether
genetic variation at "neutral" marker loci -- for example, microsatellite markers -- is an indicator of the current
fitness of a population. In theory a number of mechanisms can produce a
positive association between neutral genetic variation and fitness when
populations are compared. An association between individual heterozygosity
and fitness within natural populations (i.e. when individuals are
compared) has been known for decades (e.g. see May 2003 #409 and also
#431, below). But are
populations which are more genetically variable overall also more fit
any meaningful sense of population fitness?
Heterozygosity and DNA
fingerprint band-sharing at allozyme and RFLP loci (not microsatellites)
were estimated in paired high- and low-diversity populations of three
subspecies of gophers. All the animals were grown in the laboratory to
control for environmental effects. The mean growth rate (of body size, not
numbers) in a less-variable population was consistently less than in the
more variable population with which it was compared. In fact animals in
the less variable member of the pair grew on average only half as fast.
This may be an important
analogy for aquaculture and genetic conservation, although it should be
noted that the loss of genetic variation in the gophers studied here was
rather extreme. (See mutational meltdown March 2003#388, March
2002 #300.) firstname.lastname@example.org
435. Markers for maleness in tilapia
Identification of a
sex-determining region in Nile tilapia (Oreochromis niloticus) using
bulked segregant analysis. 2003. Lee, B.-Y., D. J. Penman and T. D. Kocher. Animal Genetics
The authors used a procedure called bulked segregant analysis to search
for microsatellite marker genes associated with phenotypic sex. (In BS analysis DNA from many individuals with the same phenotype is
pooled and compared to a pool of DNA
from a contrasting phenotype. The contrast here was male vs. female
phenotypes.) Ten markers were found, all on linkage group 8, which is
therefore the (or a) putative Y-chromosome. The linkage of two markers
with the sex-determining region was so tight that the sex of offspring of
two families was correctly predicted 95% of the time.
Not always, however.
"A third family from the same population showed no evidence for
linkage of this region with phenotypic sex, indicating that additional
genetic and/or environmental factors regulate sex determination in some
families. ...These microsatellite markers ... could eliminate the tedious
process of progeny-testing males during the production of YY-supermales."
See Dec 2002 #367 for another approach to the problem of identifying sex
chromosomes in niloticus. Download the PDF from http://hcgs.unh.edu/staff/kocher/pdfs/lee.2003a.pdf
434. When are you able to see MHC
Perspective: detecting adaptive molecular
polymorphism: lessons from the MHC. 2003. Garrigan, D. and P. W. Hedrick. Evolution
This paper includes an
insightful review of current thinking about natural selection on the major
histocompatibility locus (MHC), which is thought to induce an important evolutionary
response to disease in fishes and other vertebrates (e.g.
Mar 2002 #302, Jan 2003 #381, Mar 2003 #398). The main focus of the paper
is an evaluation of the power of the usual statistical apparatus to reject
a null hypothesis of selective neutrality. The MHC is here used
philosophically as an alternative null hypothesis in which balancing
selection can be assumed.
The news is not good for people who would be unhappy with a
result (i.e. anyone applying for grant renewal). "We find that selection is not detectable in MHC datasets in
every generation, population, or every evolutionary lineage. This suggests
either that selection on the MHC is heterogeneous or that many of the
current neutrality tests lack sufficient power to detect the selection
consistently. Additionally, we identify a potential inference problem
associated with several tests of neutrality. We demonstrate that the
signals of selection may be generated in a relatively short period of
microevolutionary time, yet these signals may take exceptionally long
periods of time to be erased in the absence of selection. This is
especially true for the neutrality test based on the ratio of
nonsynonymous to synonymous substitutions. Inference of the nature of the
selection events that create such signals should be approached with
caution. However, a combination of tests on different time scales may
overcome such problems." email@example.com
433. Fluctuating asymmetry reflects (mainly) recent developmental history
The ontogeny of fluctuating
Kellner, J. R. and R. A. Alford. American Naturalist 161:931-947.
(FA: random developmental differences between the left and right sides of
an organism, such as bristles on the abdomen of a fruit fly) is,
potentially, a useful indication that something in the life of the animal
is not going well. See Jan 2003 #378 for an example. FA may be induced by genetic stress such as
inbreeding, or environmental stress such as high temperature. But what
developmental processes actually cause an increase in random asymmetry
and why do they vary?
about the ontology of FA were examined by applying hunger and crowding
stresses to some unfortunate lab chickens. The authors conclude that,
"asymmetry in domestic fowl is not the product of events over their
entire growth history but is influenced mainly by developmental noise in
the recent past. This suggests that elevated levels of asymmetry within a
population are likely to result from a present or very recent stress and
are not the cumulative effects of previous stresses or the effects of
stress during a critical stage in early development." They point out
that FA may be useful for monitoring current environmental
conditions. This agrees with the conclusion of another paper cited here,
Feb 2002 #293. firstname.lastname@example.org
432. Growth-maturation tradeoff in trout
The genetic architecture of
correlations among growth related traits and male age at maturation in
rainbow trout. 2003.
Martyniuk, C. J., G. M. L. Perry, H. K. Mogahadam, M. M. Ferguson and R.
G. Danzmann. Journal of Fish Biology 63:746-764.
Two important commercial
strains were studied here, Rainbow Springs and Spring Valley. Rapid growth
and early maturation are genetically correlated, implying that selected
fast-growing individuals will produce offspring which are more likely to
mature early (as two year olds), and vice versa. See #440, above. This is an important
result for aquaculture breeding programs, as is the finding that
heritabilities were moderate to high for growth, maturation and condition
factor. Linkage groups (i.e. parts of chromosomes) were identified which
contain QTLs for growth and, probably, precocious maturation. email@example.com
431. Genetically variable offspring
are predictably more fit
Prediction of offspring fitness
based on parental genetic diversity in endangered salmonid populations. 2003. Primmer, C. R., P.-A. Landry, E. Ranta, J. Merilä, J. Piironen, K.
Tiira, N. Peuhkuri et al. Journal of Fish Biology 63:909-927.
For about 1/4 century we
have known that individual heterozygosity (a measure of genetic variation)
is positively associated with individual fitness in wild populations of
many species. The explanation is still somewhat controversial (e.g. Jan
2002 #276), and many more factors may be involved than were envisaged when
the phenomenon was first noticed (e.g. MHC; Jan 2003 #381), but the
observation underlies a lot of current thinking the proper management of
endangered populations. (See #436, above.)
This paper puts a new twist on the practical
application of heterozygosity/fitness relationships by showing that it can
be used to predict the genetic diversity of offspring from the
parental genotypes. This is not as obviously true as one might think
because of the likely occurrence of very unequal reproductive success,
weird self-selection of mates based on MHC (Jan 2003 #381), etc.
The authors calculated
the expected microsatellite diversity of all possible offspring from
designated pairwise matings in several salmon populations. Predicted
heterozygosity and other diversity measures correlated well with the
observed heterozygosity of the offspring and also with offspring
population fitness traits, including egg survival and foraging behaviour.
The procedure might be useful when deciding which breeders should be
paired for mating in aquaculture production or stock enhancement. firstname.lastname@example.org
430. Fitness QTL in a wild
A genome scan for quantitative
trait loci in a wild population of red deer (Cervus elaphus). 2002. Slate, J., P. M. Visscher, S. MacGregor,
D. Stevens, M. L. Tate and J. M. Pemberton. Genetics 162:1863-1873.
This paper appears to be
the first to report QTL for a fitness-related trait (birth weight) in a
wild, free-ranging population of mammals other than people. It was made
possible by the accumulation of several
generations of pedigree data on the red deer living on the Isle of Rum,
Scotland (See Nov 2000 #132). Two methods of QTL identification are used.
In one the phenotype of an offspring is regressed against
the probability that it has inherited a QTL (actually, the QTL marker);
this is repeated for markers located over the whole genome. The
second method is a type of analysis of variance. The 93 markers used
covered an estimated 62% of the genome.
several QTLs on different linkage groups was found, one of which was
significant at the genome-wide level (i.e. it exceeded the stringent
confidence-limit required by a large number of simultaneous tests).
The QTL effects are surprisingly large, given the "Fishererian"
expectation that most of the additive variance for fitness traits should
be eliminated by natural selection. The authors discuss recent evidence
that there is actually a lot of additive genetic variance but that
heritability of fitness traits remains low because there is even more
non-additive variance. Some of the evidence has been noted on this GCL
website (Feb 2000 #10). email@example.com
429. How to estimate migration and Ne
Estimating effective population
size and migration rates from genetic samples over space and time. 2003.
Wang, J. and M. C. Whitlock. Genetics 163:429-446.
Here, at last, are
procedures which can be used to estimate
effective population size and migration rate simultaneously, from a set of
samples taken from a population at different times. Earlier methods for
estimating the variance effective population size, Ne, from changes in
marker allele frequencies have been constrained by the assumption that no
immigration takes place (also, that no direct selection on the markers
takes place). The immigration assumption is utterly unreasonable in many
small populations. Indeed, the immigration rate is often the most
significant genetic feature of such populations in a conservation context
(e.g. Aug 2002 #342, May 2003 #400).
previous moment and maximum-likelihood methods to allow the joint
estimation of Ne and migration rate (m) using genetic samples over space
and time. It is shown that, compared to genetic drift acting alone,
migration results in changes in allele frequency that are greater in the
short term and smaller in the long term, leading to under- and
overestimation of Ne, respectively, if it is ignored." The computer
program MLNE which does this can be downloaded from http://www.zoo.cam.ac.uk/ioz/software.htm along with other useful
programs (such as the one mentioned in May 2002 #320).
428. Evaluating the success of
Evaluation of the genetic
management of the endangered black-footed ferret (Mustela nigripes). 2003. Wisely, S. M., D. B. McDonald and S. W. Buskirk. Zoo
There aren't many
detailed, genetic analyses of the success of a genetic conservation
program -- lots of suggestions of how to mange the breeding, but not a lot
of follow-up. Of course in fisheries there has rarely been time for
follow-up (but see June 2000 #61, Jan 2001 #158, Feb 2001 #163). The captive population studied in this paper has been managed
according to the "minimal kinship selection" principle for many
generations (MKS; Jan 2002 #283, Aug 2002 #335). There were only seven
founders contributing genes to the captive population -- comparable to a
lot of dead-but-walking salmon on the march to extinction.
data gave an accurate but only moderately precise estimate of
to pedigree records] . Genetic diversity was similar in captive populations
maintained for breeding and release. ... Wild-born individuals from
reintroduced populations maintained genetic diversity and avoided close
inbreeding. [There was] small but
measurable genetic differentiation between the reintroduced populations [founder
effect] . The
model of random mating predicted only slightly lower levels of
heterozygosity retention compared to the [MKS] strategy. The random mating strategy may be a
viable alternative for managing large, stable, captive populations such as
that of the black-footed ferret. firstname.lastname@example.org
427. Competition difficulties in genetic and breeding programs
Genetic architecture and
evolutionary constraint when the environment contains genes.
2003. Wolf, J. B. Proceedings National Academy of Science (US)
It is obvious that
competition and other social interactions among fish affect their growth,
maturation and survival. Such interactions are very rarely taken
into account in the design of genetic experiments, e.g. for estimating
heritability, or in the design of selection programs.
The oversight is so serious
that (in my opinion) many heritability estimates may be wrong and designs
based on them likely to fail (Sep 2000 #109, Aug 2002 #343). This is
especially likely to be true of the more sophisticated
"classical" breeding programs which use heritability estimates
to make crucial selection decisions. "Theory [reviewed in the paper] has shown
that these [indirect, competitive] effects modify the definition of genetic
architecture by making the phenotype the property of the genotypes of
multiple individuals and alter evolutionary dynamics by introducing
additional heritable components contributing to trait evolution."
The author of this paper
has written a theoretical formulation of the social effects which is
useful for REML analysis. The accompanying growth experiments were
performed on Drosophila. There was indeed a genetic variance component due to the genotypes of other individuals in the population and
which was hidden from ordinary genetic analysis. The author found that the
expected negative covariance between direct and indirect (competitive)
genetic effects, such that genes which make an individual bigger make
other individuals smaller, is surprisingly large. Furthermore, the effect
increases as the genetic relatedness of individuals in the competing group increases.
A couple of practical
points would seem to follow from this: (1) everything possible should be
done to reduce competition in aquaculture selection programs (more
precisely, to prevent competitive behavior being rewarded by increased
growth or reproductive success), and (2) assuming that point (1) is acted
upon, within-family selection may be the most effective selection scheme
for developing a strain of tame, non-competitive animals which ignore each
other and feed all the time. This is another boost for within-family
selection (see Feb 2002 #293). email@example.com