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.
479. Re-introduced salmon retain genetic diversity
Comparison of genetic diversity in the recently founded Connecticut
River Atlantic salmon population to that of its primary donor stock,
Maine's Penobscot River. 2004. Spidle, A. P., T. L. King and B. H.
This paper on salmon
supplementation is refreshing because the authors do not conclude
that the sky is falling and we're all gonna die. Salmon in the
Connecticut River (USA) were extirpated and then, more than 100 years
later, the river was re-populated with stock from the Penobscot River in Maine. The
current Connecticut River sea-run salmon are still almost entirely dependent on
hatchery breeding. This survey shows two things: (a) the Connecticut and
Penobscot populations have diverged genetically, whether from drift or
selection we do not know, and (b) heterozygosity and allele number (and
inferred effective population number) is comfortably high in the
Connecticut River at the present time.
River restoration therefore contains a large percentage of the maximum
genetic diversity that could be extracted from its source population, and
a typical amount of genetic variation for a population from the drainage
of a major river." Also, "Healthy ratios of Ne to N indicate
that hatchery production has not resulted in excessive inbreeding to
date." A couple of theoretical papers have predicted this happy outcome, Feb 2002 #297 and June 2002 #327. For
another successful supplementation see Jan 2001 #158. firstname.lastname@example.org
genetic diversity reduces the severity of epidemics
The contribution of genetic diversity to the spread of infectious
diseases in livestock populations. 2003. Springbett, A. J., K. MacKenzie,
J. A. Woolliams and S. C. Bishop. Genetics 165:1465-1474.
Hatchery managers are
well aware that genetic
diversity in an aquacultural broodstock should make it more
resistant to disease. The explanation for this is not so well
understood, by aquaculturists or anyone else. (Various mechanisms by which
disease selects for diversity at the major histocompatibility complex in
fish, MHC, have been mentioned several times here: Jan 2003 #381, Mar 2003
#398, May 2003 #409).
In this simulation study,
genetic diversity is represented by the number of different genotypes
which convey resistance to a pathogen. Several different genetic and
population dynamic models are investigated. The output of the simulation
is the severity and frequency of epidemics. The general conclusions are of
considerable practical interest: (1) genetic diversity does not decrease
the frequency of epidemics and may even make minor epidemics more
frequent. However, (2) catastrophic epidemics are much less
frequent and probably don't last quite as long, and there is less
disease-related mortality during such epidemics. Also, generally speaking,
(3) there are fewer infected animals at any given level of pathogen
pressure in a genetically diverse population. See #468, below. email@example.com
477. Negative genetic correlation
among shrimp reproduction traits (?)
Genetic parameter estimates for reproductive traits and egg
composition in Pacific white shrimp Penaeus (Litopenaeus) vannamei. 2004.
Arcos, F. G., I. S. Racotta and A. M. Ibarra. Aquaculture 236:151-165.
The following traits are
analysed in this paper (full-sib heritabilities only): days to first spawn
after ablation, egg diameter and number, egg triglycerides, vitellin,
total protein and total lipids. All traits except total lipid were
heritable and thus presumably selectable. However, "Surprisingly,
large negative genetic correlations were estimated between females' total
weight with vitellin (-0.62). Negative genetic correlations were also
obtained for days to first spawn and vitellin (-0.35) and triglyceride
(-0.30)." These traits are all of aquacultural significance.
Since rapidity of
spawning is useful, the negative correlation between egg quality traits
and days to first spawn is advantageous. The negative correlations between
the egg quality traits and female weight may be more of a problem
however, if they are also found in half-sib analyses. As noted in an
e-mail from A.M. Ibarra, "Then, the question is, for spawners of the
same age, are the larger females (or those producing the largest numbers
of eggs) also the 'best mothers'?" If not, this genetic correlation
have to be taken into consideration in the design of selection programs,
e.g. by selecting deviates from the correlation. firstname.lastname@example.org
476. How to keep numbers up and inbreeding down in supplemented stocks
Maximizing offspring production while maintaining genetic diversity
in supplemental breeding programs of highly fecund managed species. 2004.
Fiumera, A. C., B. A. Porter, G. Looney, M. A. Asmussen and J. C. Avise.
Conservation Biology 18:94-101.
In aquaculture, as in
stock supplementation, one generally needs to produce as many offspring as
possible every generation. One also wants to minimize inbreeding and
random loss of genetic diversity. (See #479, above.) Although the latter two, genetic,
objectives are closely related they are not necessarily maximized by the
same mating design. Furthermore, they often conflict with the demographic
objective of maximizing the census number of offspring. The genetic
advantage of equalizing the number of offspring from all potential
breeders, both male and female, is well known to hatchery managers, but it
can seriously interfere with total production.
The authors of this paper
investigated, by computer simulation, "four basic supplemental
breeding designs involving either monogamous pairings or complete
factorial designs (in which every female is mated to every male and vice
versa), each with or without the added stipulation that all breeders
contribute equally to the total reproductive output. In general, complete
factorial designs that did not equalize parental contributions came
closest to the goal of maximizing offspring production while still
maintaining relatively large effective population sizes." The
factorial design worked particularly well when some of the breeders were
effectively sterile "duds", as is often true in aquaculture. email@example.com
tilapia are more resistant to Aeromonas
Disease resistance of Nile tilapia (Oreochromis niloticus), blue
tilapia (Oreochromis aureus) and their hybrid (female Nile tilapia×male
blue tilapia) to Aeromonas sobri. 2004. Cai, W.-q., S.-f. Li and M.
Jiang-yao. Aquaculture 229:79-87.
Of the three genotypes
mentioned in the title the hybrid was in general the most resistant to
injection with Aeromonas, and pure O. aureus the least resistant.
"The hybrid (female Nile tilapia X male blue tilapia) had a better
performance in three disease resistance parameters: median lethal dose
(LD50), erythrocyte C3b receptor aggregates, and percentage of phagocytic
leukocyte. In the aspect of percentage of erythrocyte active rosette (EaR)
of T lymphocyte, the hybrid was intermediate to the Nile tilapia and blue
tilapia; For the other two traits, total amount of complement and
alternative pathway of complement (C3 shunt), the hybrid showed no
significant difference from Nile tilapia and blue tilapia." This is a
useful, practical result because hemorrhagic septicemia caused by A.
sobri can be a serious problem in aquaculture. firstname.lastname@example.org
species introductions might be "inbreeding depressed"
Hatching failure increases with severity of population bottlenecks
in birds. 2004. Briskie, J. V. and M. Mackintosh. Proceedings National
Academy of Sciences USA 101:558-561.
This is a species-level
comparison of bird populations in New Zealand which have been bottlenecked
to varying degrees, some very severely. Bottleneck sizes were estimated
from census records, not inferred from neutral genetic markers, and
hatching failure rates were estimated from field observations by these
authors and many others. The inferred minimum population size which causes
a long-term reduction in hatchability (presumably due to inbreeding) is
surprisingly large -- 150 individuals. In fact, as many as 600 founders
may be needed to eliminate inbreeding depression when a species is
introduced. The semi-log
scattergrams of hatching failure vs. bottleneck (or founder) number
are immediately convincing and are supported by a conscientious statistical
The cause is presumably inbreeding depression although the authors could not entirely exclude the
possibility that causality flows the other way Down Under, i.e. that
species with naturally poor hatchability are more likely to have
experienced bottlenecks in New Zealand. Are these results important? The
authors note, "A worldwide review of about 700 translocations [of
breeding plan that minimizes inbreeding
Fixed contributions designs vs. minimization of global coancestry
to control inbreeding in small populations. 2003. Fernández, J., M. A.
Toro and A. Caballero. Genetics 165:885-894.
Various breeding schemes
have been proposed to minimize inbreeding and conserve genetic diversity
in small populations. This paper presents the results of various computer
simulations in which the minimization of global coancestry does the best
job in the short and medium term. (This is very close to minimal kinship
selection; Nov 2001 #261, Jan 2002 #283, Aug 2002 #235.) The authors
"also investigate the performance of the alternative methods against
departures from the ideal conditions, such as inbred or differentially
related base individuals and random failures in the expected
contributions. The method of minimization of global coancestry turns out
to be more flexible and robust under these realistic situations". See
Aug 2001 #212, by the same authors, for a review of the interrelationships
between effective population size, coancestry and other statistics derived
from pedigree records. See Feb 2004 #455 for another breeding plan. email@example.com
472. Useful shrimp (P. monodon) microsatellites
Development of microsatellite markers in black tiger shrimp (Penaeus
monodon Fabricius). 2003. Wuthisuthimethavee, S., P. Lumubol, a.
Vanavichit and S. Tragoonrung. Aquaculture 224:39-50.
microsatellites are described which are likely to be useful population and
pedigree markers for P. monodon. The sequences of all these
microsatellites have been placed in GenBank and accession numbers are
provided in the paper. firstname.lastname@example.org
have the big horns gone?
Undesirable evolutionary consequences of trophy hunting. 2003.
Coltman, D. W., P. O'Donoghue, J. T. Jorgenson, J. T. Hogg, C. Strobeck
and M. Festa-Bianchet. Nature 426:655-658.
People who shoot rams for
trophies are altering the balance of sexual selection in bighorn sheep.
Big males with extra-large horns have an advantage when competing for
females, but find it hard to deploy these natural assets when they've been
shot and stuffed. The authors analyse the effect of trophy hunting on a
population of Ovis canadensis in Alberta, Canada, using partial pedigree
information inferred from markers, trophy records and field work. The
paper is a good example of how one can use family relationships inferred
from microsatellite markers to generate estimates of genetic
heritabilities and correlations in wild populations.
The authors found that
"... trophy-harvested rams were of significantly higher genetic
'breeding value' for weight and horn size than rams that were not
harvested. Rams of high breeding value were also shot at an early age, and
thus did not achieve high reproductive success. Declines in mean breeding
values for weight and horn size therefore occurred in response to
unrestricted trophy hunting, resulting in the production of
smaller-horned, lighter rams, and fewer trophies." email@example.com
470. Differences in growth and shape among tilapia strains
Comparison of growth, fillet yield and proximate composition
between Stirling Nile tilapia (wild type) (Oreochromis niloticus, Linnaeus)
and red hybrid tilapia (Florida red tilapia X Stirling red O. niloticus)
males. 2003. Garduño-Lugo, M., I. Granados-Alvarez, M. A. Olvera-Novoa
and G. Muñoz-Córdova. Aquaculture Research 34:1023-1028.
In summary, this
comparison of males from the two species/strains gave the following
results: the red hybrid had higher survival (97% vs. 83%), final
body weights at 98 days (473g vs. 349 g). Fillet yields were
approximately 33% for both strains but fresh fillet lipid content was very
different, 0.33% vs. 2.1% [!]. firstname.lastname@example.org
number of markers you need increases as the log of population size
Balancing population size and genetic information in parentage
analysis studies. 2003. Jones, B. Biometrics 59:694-700.
Larger populations (broodstocks)
include more families, in general. If genetic markers are used to
distinguish families (Dec 2003 #451, #449), the accuracy with which
offspring can be matched with their parents is influenced by the
population size and the number and polymorphism of the markers. When
designing a broodstock program which uses genetic markers to identify
parent-offspring combinations, one should know in advance how many markers will be needed.
In some (but not all)
maximum-likelihood assignment programs (CERVUS, for example) offspring
which cannot be matched to parents with sufficient confidence are dropped.
But this is unsatisfactory if one cannot identify enough families to
achieve the purpose of the study, such as heritability estimation,
breeding value estimation or mean kinship estimation. Can one evaluate a
particular situation in advance to decide how many markers are needed?
It is shown in this paper
that the number of loci needed to assign all offspring correctly is
proportional to the logarithm of the population size. The accuracy of
assignment is not affected by the distribution of family sizes. The log
relationship also holds true at any (constant) level of uncertainty about
assignment accuracy. The constant of proportionality will probably have to
be determined empirically (publications on that topic from people who
already have the requisite data would be most welcome). email@example.com
468. Lots of natural genetic variation for disease resistance
Genetic basis of natural variation in D. melanogaster antibacterial
immunity. 2004. Lazzaro, B. P., B. K. Sceurman and A. G. Clark. Science
The reduced frequency of catastrophic epidemics in populations which have genetic variability for resistance to
pathogens is demonstrated in #478, above. Although many genes that affect
disease resistance have been identified in arthropods very little is known
about their variation in wild or aquacultural populations. In this study
of wild Drosophila considerable polymorphism was observed in the ability
to resist infection by the Gram-negative bacterium Serratia marcescens.
"Variability in immune competence was significantly associated with
nucleotide polymorphism in 16 innate immunity genes, corresponding
primarily to pathogen recognition and intracellular signaling loci, and
substantial epistasis was detected between intracellular signaling and
antimicrobial peptide genes." For related, pathogen resistance genes
in shrimp see Sep 2001 #233, Mar 2002 #302, Jan 2003 #377, Dec 2003 #453;
for vertebrate MHC diversity see Jan 2003 #381, Mar 2003 #398, May 2003
#409, Oct 2003 #434. firstname.lastname@example.org
diversity information on cultured tilapia
Genetic diversity in farmed Asian Nile and red hybrid tilapia
stocks evaluated from microsatellite and mitochondrial DNA analysis. 2004.
Romana-Eguia, M. R., M. Ikeda, Z. U. Basiao and N. Taniguchi. Aquaculture
This paper provides a
much-needed survey of neutral marker diversity in several popular Asian
strains of Oreochromis niloticus and niloticus X mossambicus hybrids. The
GIFT strain (Philippines) had the highest expected heterozygosity, as
would be expected from its recent origin as a multi-continent broodstock
synthesized for starting a selection program. The Genetically Male Tilapia
(GMT) strain had the lowest heterozygosity, as would be expected from its
birth in a multi-generation sequence of chromosome manipulations (Dec 2003
#452). The differences in heterozygosity among strains were largely
paralleled by differences in allele number. Genetic distance dendrograms
are presented and explained in relation to the interesting history of
Most of the samples have
a strong excess of homozygotes, which the authors interpret as inbreeding
caused by management problems (multilocus disequilibria were not reported
so the authors evidently mean current, not historical inbreeding). The
NIFI strain was an exception. Microsatellite loci were more informative
than mitochondrial RFLP markers, as expected, and all the technical primer
and amplification information is available. The markers used here would be
good candidates for a "standard set" which would allow tilapia
researchers to compare their results. email@example.com
to find markers that are under selection
DetSel 1.0: a computer program to detect markers responding to
selection. 2003. Vitalis, R., K. Dawson, P. Boursot and K. Belkhir.
Journal of Heredity 94:429-431.
This easy-to-use program
attempts to identify marker loci that are selected differently in paired
populations. Loci identified as possibly affected by selection are
outliers in the multilocus F distribution which would be expected under a
neutral, random drift model. (F, the inbreeding coefficient, is here an
estimate of identity by descent, i.e. the probability that two alleles
sampled in a population are descended from the same ancestral gene). One potential application is to prevent non-neutral loci from
biasing estimates of population parameters such as effective population
size. This program and related outlier analyses, such as those based on FST or FIS, could also be useful when the objective is genetic
conservation (evolutionarily significant population units might have a lot
of selected loci), or aquaculture genetics (identifying adaptive loci or
markers for artificial selection). But one must be careful;
many precautions must be taken to avoid becoming seduced by false
positives. The program is available free at http://www.univ-montp2.fr/~genetix/detsel/detsel.html.
Author email firstname.lastname@example.org