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.
623. Selection schemes for socially interacting broodstocks
Genetic improvement of traits affected by interactions among individuals: sib selection
schemes. 2007. Ellen, E. D., W. M. Muir, F. Teuscher and P. Bijma. Genetics 176:489-499.
Interactions among individuals is of great importance to the growth and survival of most animals. Two papers highlighted earlier (Mar-Apr 2007 #597 & #600) describe a method for including the heritable component of social interaction in conventional additive genetic
models of growth. A whole additional level of genetic variance becomes available for selection when interactions are taken into account. This new paper examines several practical selection schemes
for making use of both individual and interaction genetic variances. Very intriguing for the design of aquaculture selection programmes. email@example.com
622. More infectious, more disease-causing, and more likely to kill
Local interactions select for lower pathogen
infectivity. 2007. Boots, M. and M. Mealor. Science 315:1284-1286.
Aquacultural broodstocks are interconnected throughout the world by suppliers of breeders and "seed". Although there are restrictions on the importation of
such genetic products in some jurisdictions the rate of world-wide transfer is
probably increasing rather than decreasing for tilapia and shrimp.
Theory suggests that one unfortunate side effect of this may be that pathogens evolve to be more infective. The essence of the theory is that when animals move more frequently between populations the pathogens they carry are more likely to find themselves surrounded by non-infected individuals, and pathogens encounter a larger number of susceptible hosts. Pathogens are thereby selected for enhanced infectivity. The same
logic applies if individuals are suddenly able to mingle more freely within
The prediction in this paper is based on game-theoretic analysis of a strategy termed "prudence".
An elegant little experiment shows that the prediction is correct. A mixture of infected and non-infected caterpillars was placed in a series of artificial media which differed in viscosity. In some containers the medium was quite liquid, allowing the caterpillars to move about freely, and in other containers it was viscous, causing the caterpillars to separate into groups.
After 40 weeks the pathogen (a virus spread by cannibalism) was assayed for infectivity. The virus in the medium which restricted movement of hosts had evolved to be about two-thirds less infective. "As populations become more mixed, we might expect that not only will there be an increase in the extent of disease outbreaks but also the potential emergence of more infective strains of parasites."
A commentary by Angus Buckling in the same issue of Science puts it this way: "Regardless of the precise details of the theoretical explanation, there is now, for the first time, some very convincing experimental data that parasites are likely to evolve to be less prudent when they get to travel. Less prudent can mean various things: more infectious, more disease-causing, and more likely to kill. None of which is likely to be very good for hosts." firstname.lastname@example.org
621. Temperature affects Penaeus gene
Stress-induced gene expression profiling in the black tiger shrimp Penaeus
monodon. 2007. de la Vega, E., M. R. Hall, K. J. Wilson, A. Reverter, R. G. Woods and B. M. Degnan.
Physiological Genomics in press.
One has the overall impression that shrimp are more affected by low oxygen and adverse temperatures than by changes in salinity, and this study on P. monodon confirms this at the level of gene expression. A microarray chip (see Dec 2003 #441 on microarrays) was loaded with cDNA from genes which are expressed differently (up- or down-regulated)
in stressful and normal conditions. As usual at this point in our
understanding of the universe most of those genes (72%) are not similar to any known
genes -- in other words we have very little idea what three-quarters of the genes that
reacted to stress are doing.
However, "Among those genes with high identity to known sequences, the most common functional groups were immune related genes and non-Long Terminal Repeat (nonLTR) retrotransposons." Why the polymerase (POL) retrotransposon sequences should be
differently regulated under stress is totally obscure at this point, although the same thing happens in people, chickens etc. The authors
also say "there is no evidence of transposition or regulation of surrounding genes".
Anyway, "Hypoxic and hyperthermic stressors induced the most severe short-term response in terms of gene regulation, and the osmotic stress had the least variation in expression profiles relative to the control". See Dec 2006 #573, Feb 2004 #465. email@example.com
620. Tilapia growth trial at two feed levels
Performance of genetically improved Nile tilapia compared with red hybrid tilapia fed diets containing two protein
levels. 2007. Ng, W.-K. and R. Hanim. Aquaculture Research 38:965-972.
The GIFT strain had a higher growth rate
in these trials and, consequently, a better food conversion ratio (FCR) than
a local red hybrid tilapia at both 25% and 35% protein. The increase from 25% up to 35% protein increased the growth rate of GIFT but not of the local reds. This genotype-environment interaction illustrates a general observation about genetic improvement: an improved strain is better able to take advantage of an improved environment. (Or, to look at it the other way around, putting an improved strain in an inferior environment is a waste of opportunity.)
The local red strain in
Vietnam is thought to be a mixture of mossambicus and niloticus. It is selected for its coloration but little is known about its genetics. The authors write that they used a restricted feeding regime (4% body weight per day) but it is not clear whether the fast growing strain actually received more food in terms of absolute quantity once it had become somewhat larger. To this extent the interpretation of the FCR result is somewhat ambiguous. See May 2001 #198 for selection response of appetite, see Feb 2007 #580 & Jan 2000 #72 for tilapia strains. See
also #615 below. firstname.lastname@example.org
619. How to correct family bias in genetic distance estimates
Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in
California. 2007. Bucklin, K. A., M. A. Banks and D. Hedgecock. Canadian Journal of Fisheries and Aquatic Sciences 64:30-42.
To qualify for protection in the United States under (Richard Nixon's!) Endangered Species Act, a population needs to be "distinct". Distinctiveness in this context implies, among other
things, being genetically distant from other populations.
This paper describes a procedure for increasing the accuracy of genetic distance and related variance estimates when samples contain significant proportion of brothers and sisters. This can happen when populations are very small or when families only are sampled. A conceptually similar bias occurs when there is an unrecognized admixture of populations (the Wahlund effect).
The procedure, described here
for use on coho salmon but widely applicable, is especially useful when juveniles (which often include groups of related individuals) have to be collected instead of adults,
which are more likely to be well mixed.
Basically, what the authors did was identify sib groups based on relatedness (see Dec 2006 #572) and then replace the groups with their inferred parents in the subsequent statistical analyses. This adjustment improved, (that is, reduced) the estimates of hidden admixture of populations within collections, and it also improved (increased) the estimated genetic distance among populations.
The improved analysis has consequences. After the adjustment, "...we find strong concordance of genetic and geographic distances.... [and that] stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding." email@example.com
618. Relatively few spawners support Australian prawn fishery
The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus
esculentus). 2007. Ovenden, J. R., D. Peel, R. Street, C. A.J., H. S.D., P. S.L. and P. H. Molecular Ecology 16:127-139.
It seems that
surprisingly few spawners are supporting the vigorous Australian fishery for the brown tiger prawn (Penaeus esculentus). This is the conclusion reached in this analysis of microsatellite variation in three, successive annual samples taken off the east coast of Australia.
Several statistical techniques were used to estimate short- and long-term
effective population number (Ne; see May 2002 #313, Nov 2006 #553) all indicating effective population sizes between one and ten thousand, with lower confidence limits greater than 300. The fishery, or census, population is of course much much larger.
As the authors point out this value for Ne is large enough to keep random drift to low levels in the usual population genetic models. The minimal safe Ne is conventionally taken to be 50 but has been shown to be much larger. One wonders about vulnerability to local environmental disruption, and, of course, overfishing of a critical age group, both of which might draw the prawns into a genetically mediated extinction vortex (May 2003 #400, June 2001 #210) . The species has been shown to be genetically heterogeneous over its range in Australia.
The authors also say "We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders". firstname.lastname@example.org
617. A QTL marker which didn't work in the real world
The utility of QTL-Linked markers to detect selective sweeps in natural populations — a case study of the EDA gene and a linked marker in threespine
stickleback. 2007. Cano, J. M., C. Matsuba, H. Mäkinen and J. Merilä. Molecular Ecology 15:4613-4621.
One hopes and expects that quantitative trait loci (QTL) which have large effects under experimental conditions will be important in nature as well. One also
wants microsatellites that are closely linked to QTL in breeding (mapping) experiments
to act as markers for these QTL in nature. But this doesn't
This paper shows that, as expected from previous work, a QTL which has a large effect on the number of lateral plates of sticklebacks shows sequence variation among wild populations. The variation in the coding region of the QTL is functional,
is under selection and the distribution of alleles correlates well with the observed morphological variation. Unfortunately, a microsatellite marker which is very informative in experimental crosses, owing to its tight linkage with the QTL, wasn't
informative at all in this real world situation where, the authors show, there is recent or ongoing selection for plate morphology.
The distribution of marker alleles "did not differ from that of neutral markers and, was therefore unable to detect the signature of natural selection responsible for population divergence". Why not? The authors say there are two reasons: (1) the marker was not quite close enough to the QTL (>0.5 cm), even though it was highly informative for mapping purposes, and (2) since plate number is actually polygenic, covariances among marker loci will in theory be more informative than frequencies at loci,
or markers for QTL, considered one at a time. email@example.com
616. One genotype is good enough for the albatross
Surviving with low genetic diversity: the case of
albatrosses. 2007. Milot, E., H. Weimerskirch, P. Duchesne and L. Bernatchez. Proceedings of the Royal Society (B) 274:779-787.
Two species of albatross, the wandering and Amsterdam albatrosses, have been found to have very low levels of genetic (AFLP) diversity. The authors surmise
that albatrosses inherited this deficit from their last common ancestor about 0.8 M year ago. The genetically more diverse species has "approximately one-third of the minimal values reported in other vertebrates". The other species was half as low again. "Given the generally high breeding success of these species, it is likely that they are not suffering much from their impoverished diversity. Whether albatrosses are unique in this regard is unknown, but they appear to challenge the classical view about the negative consequences of genetic depletion on species survival." firstname.lastname@example.org
615. Tilapia strains compared at two stocking densities
Comparative study of growth performance of three strains of Nile tilapia, Oreochromis niloticus, L. at two stocking
densities. 2006. Ridha, M. T. Aquaculture Research 37:172-179.
The Freshwater Aquaculture Center in Kuwait has compared a strain of tilapia called FaST, produced by within-family selection in the Philippines, with GIFT, also developed in the Philippines, and
with a non-selected control (Ismaelia strain from the USA). At low stocking density the FaST selected line had better daily growth rate, specific growth rate, feed conversion ratio and gross yield than GIFT, which was in turn better than the control. At high densities GIFT was non-significantly better than FaST.
There was thus significant genotype X environment (strain X density) interaction for the performance variables but the nature of this interaction was not examined statistically. Inspection of the data table shows that the performance of the FaST selected line shows a stronger response to environmental improvement (i.e. lower density) than do GIFT or the control strain. See
#620, above. email@example.com
614. Markers can increase intensity of challenge-test selection
Within-family marker-assisted selection for aquaculture
species. 2007. Sonesson, A. K. Genetics Selection Evolution 39:301-317.
In aquaculture you often need to select breeders solely on the basis of information
about their siblings -- when using disease challenge test data for example.
One of the many inefficiencies of this
so-called "family selection" approach is that all members of the families have the same estimated breeding value. You can not see or select for approximately half of the genetic variance
(the variance within families) which is theoretically available for genetic
gain. If, however, you have genetic markers which are known to be associated with disease resistance (or survival, or any other family-selected trait such as fillet percentage) you may be able to use this information to select superior individuals within selected families.
This useful paper describes a breeding plan for doing this and for estimating breeding values. Simulation is used to draw some conclusions about its effectiveness. As one might expect, marker assisted selection (MAS) is most useful when the marked loci contribute a good proportion of the total variance (QTL with large effects and intermediate frequencies).
Surprisingly (to me) "the extra response due to MAS was somewhat lower for schemes with a medium heritability than with low heritability". MAS also reduces inbreeding a bit for an interesting reason which is explained in the text. The author points out that her technique potentially extends the walk-back selection procedure (July 2006 #512) to include traits which can only be measured on siblings. firstname.lastname@example.org
613. Inbreeding causes fry deformity in salmonids
Evidence for reduced genetic variation in severely deformed juvenile salmonids. 2006. Tiira, K., J. Piironen and C. R. Primmer. Canadian Jour. Fisheries and Aquatic Sciences 63:2700-2707.
Inbreeding is easy to miss when it causes problems early in life. Severely deformed hatchery fry from
samples of brown trout and non-anadromous Atlantic salmon in Finland had lower standardized microsatellite heterozygosity than normal fry in this study. They also had higher internal relatedness
(a measure of parental similarity). "Our results suggest that ... high mortality of severely deformed low heterozygosity individuals in early life stages may partly explain why some studies exploring heterozygosity–fitness correlations fail to find any association." See Oct 2003 #431 and Dec 2003 #442 for other heterozygosity X fitness studies by some of the same authors. email@example.com
612. Two new programs for parental and family identification
FAMOSPHERE: a computer program for parental allocation from known genotypic pools. 2007. Carvajal-Rodriguez, A. Molecular Ecology Notes 7:213-216.
New and improved statistical and computational approaches to the problem of inferring pedigrees from genetic markers (Dec 2006 #572) continue to appear. Here are two more, based on different principles:
FAMSPHERE "models an offspring as a 2n dimensional (n = loci number) sphere with a center (the genotype) and a radius (the mutation or genotyping error allowed). Thus, an individual will be a putative parent if it falls inside the sphere of a given offspring. The model is a formalization of the exclusion method taking into account genotyping errors or mutation". http://webs.uvigo.es/acraaj/famsphere.htm
FAP is a parental exclusion program which "(a) predicts the resolving power of specific parental data sets (nuclear and mitochondrial) for unambiguously discriminating among families / groups of families, (b) assigns family of origin to progeny from genotype (nuclear and mitochondrial) data". All parental genotypes are assumed to be known.
See FAP: an exclusion-based parental assignment program with enhanced predictive functions. 2007. Taggart, J. B. Molecular Ecology Notes 7:412-415. http://www.aqua.stir.ac.uk/rep-gen/Downloads.html.
Carvajal-Rodriguez e-mail firstname.lastname@example.org