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.
"SPF" shrimp are carriers of WSSV!
Identification of white spot
syndrome virus latency-related genes in specific-pathogen-free shrimps by
use of a microarray.
2003. Khadijah, S., S. Y. Neo, M. S. Hossain, L. D. Miller, S. Mathavan
and K. J. Journal of Virology 77:10162 - 10167.
paper from Singapore is intriguing and somewhat worrisome. The authors
developed a WSSV-specific DNA microarray (See Dec 2003 #441 on microarrays) to look at the
expression of viral genes in supposedly specific pathogen free (SPF) Penaeus monodon. The SPF shrimp, developed by the BIOTEC group in
Thailand and grown there under biosecure conditions for 6 generations
without a disease outbreak, passes the standard commercial PCR test for
absence of WSSV. Microarrays
were constructed with viral DNA extracted from WSSV-infected shrimp. The
arrays included approximately 3000 clones and were developed in a sophisticated university research laboratory.
Flooding the arrays with cDNA from infected shrimp revealed the expression
of many WSSV genes, as expected. However, cDNA from the putative SPF
shrimp revealed that at least three WSSV genes were functioning in
them, too. "... hybridization with the SPF sample revealed
exceptionally high signal intensities from some elements on the array,
indicating that these shrimps had been carriers of the virus and were
actively expressing viral genes."
The WSSV genes
expressed strongly in the SPF shrimp were not among those expressed
strongly in infected shrimp, so the virus is behaving differently in these
host environments. Examination of various sequence motifs lead the authors to suggest that the genes may be transcription
factors involved in latency and pathogenesis of the virus. WSSV viral
genomes have been found in asymptomatic P. monodon before, but never in a
biosecure SPF population. The commercial single-step PCR, which
has a detection threshold of about 20 viral genomes, may not be sensitive
enough to see this stage of latent infection. The microarray is an exciting new tool for
investigating (and perhaps selecting) genes involved in viral
pathogenesis. firstname.lastname@example.org .
Extinction-recolonization genetics of a trout metapopulation
temporal changes of genetic composition in brown trout (Salmo trutta L.)
populations inhabiting an unstable environment.
2003. Østergaard, S., M. M. Hansen, V. Loeschcke and E. E. Nielsen.
Molecular Ecology 12:3123-3135.
of trout and salmon inhabiting small rivers which drain into the sea are
often arranged side by side along a coastline. Some rivers have no trout
while some do, and some rivers have no water in them during particularly
dry summers. The
situation is stable in the sense that there are always trout somewhere in
the general area. However it is unstable in the sense that individual
rivers may be trout-free from time to time. From a conservation point of
view we wish to know whether we are looking at (a) a large population
which has geographically persistent sub-populations (isolated individual
rivers), or (b) at a large "metapopulation" in which riverine
populations periodically go extinct and are recolonized from nearby
The distinction between
(a) and (b) is important. If individual riverine populations are
persistent, perhaps because the fish can survive unnoticed at river
mouths in bad years, the genetic differences among populations may be adaptive, so that each is worth conserving as an evolutionarily significant
population unit. But if the rivers are components of a larger
metapopulation then the genetic peculiarities of any particular population
reflects nothing but founder sampling effects and drift, and are of no
adaptive utility. The peculiarities may even be of negative adaptive
utility owing to accidental genetic fixation of deleterious alleles.
is an island in the Danish Baltic sea. Many small rivers run down to the
coast from a central highland. Trout scale and otolith samples from these
rivers have been collected and preserved from the late 1940s to the
present. Analysis of microsatellite diversity in historical and current
samples leads the authors to conclude that the rivers on Bornholm
represent a metapopulation, not a population with a persistent
geographical structure. "We suggest that Bornholm trout represent a
metapopulation where the genetic structure primarily reflects strong drift
and gene flow, combined with occasional extinction-recolonization
events." The authors make the following comment about conservation
strategies. "… if a river is devoid of trout this may be a natural
phenomenon, and it is still important to protect the habitat as it may
later become recolonized. … specific behavioural adaptations to low
water levels and low saline marine environments exhibited by trout from
the Bornholm and Gotland islands stresses the importance of conserving
these population systems as a whole[emphasis added].
This goal is best achieved by conserving as many filled and empty patches,
i.e. rivers, as possible." But the nice thing about a metapopulation
is that you don't need to conserve all the components.
See Oct 2000 # 115, Mar
2003 #394 for a contrasting case in New Zealand where populations of
introduced salmon appear to have evolved river-specific adaptations. email@example.com
The schedule of inbreeding affects inbreeding depression
The influence of
variable rates of inbreeding on fitness, environmental responsiveness, and
evolutionary potential. 2003. Day, S. B., E. H. Bryant and L. M. Meffert. Evolution 57:13-14-1324.
interesting experiment on house flies shows that the rate and schedule of inbreeding interact with the level of inbreeding to determine
inbreeding depression. Populations of flies from the same source (a dump
in Texas) were inbred quickly, slowly or intermittently to the same
inbreeding level, F=0.37. After this inbreeding had been achieved, the
fitnesses of the populations were compared and so was their ability to
evolve tolerance to a more stressful environment (temperature
The control population C,
which wasn't inbred at all, had the highest allozyme diversity at the end
of the experiment and also maintained the highest capacity to evolve. Population FS, which was rapidly inbred to F=0.37 during
four successive generations and then allowed to expand, had the lowest
final fitness and showed essentially no ability to respond to the
experimental evolutionary challenge. Population PC, which underwent
alternating episodes of strong and zero inbreeding, did slightly (really,
not much) better than FS. This PC protocol mimicked a serial
"founder-flush" regime in a natural population. PC inbreeding
occurs commonly in aquaculture because of the practice of founding of new
aquacultural broodstocks from existing ones (e.g. Jan 2000 #4).
The most benign
inbreeding scheme in this experiment was the slow and steady SL protocol, in which the population maintained a constant effective
population number during the inbreeding. This was the only inbred
population which retained some of its evolutionary potential. (Evidently
the bottlenecking did not convert useful amounts of epistatic variance
into additive genetic variance; Jun 2001 #207 & Oct 2000 #116.) Slow
inbreeding is the objective in well-conducted aquaculture and genetic
conservation programs -- where, of course, the inbreeding damage may
already have been done before the programs smartened up. The authors noted
a lot of variation among replicates, reflecting the chance sampling of
alleles during the inbreeding and flushing phases (see May 2003 #402). See
also Feb 2000 #17, Mar 2002 #300 for other papers on houseflies as
experimental models for genetic conservation. firstname.lastname@example.org
Successful growth selection in Kuruma shrimp
growth of selected and non-selected Kuruma shrimp Penaeus (Marsupenaeus)
japonicus in commercial farm ponds; implications for broodstock production. 2004. Preston, N. P., P. J. Crocos, S. J. Keys,
G. J. Coman and R. Koenig. Aquaculture 231:73-82.
paper describes a simple mass selection program which appears to have
worked well. The selected breeders came from the largest 10% of a
(presumably equal-aged) population in farm ponds. The offspring of the
animals were 9% - 14% larger than contemporaneous controls at first
harvest. After more generations of non-selective rearing under controlled
conditions, the descendants of the selected parents were 14% larger than
An important finding of
this study, emphasized by the authors, is that "stocks of P.
japonicus, initially selected for high growth in farm ponds and then
reared from egg to adult for three generations under controlled conditions
in tanks, retained their capacity for superior growth when returned to
farm ponds. This indicates that selected lines, maintained in bio-secure
conditions, could provide reserve stocks for re-establishing superior
lines of farm stocks. In some circumstances, this may be an appropriate
strategy for producing all the progeny required for stocking ponds." email@example.com
Exploited cod population changes its genetic identity
of archived samples indicates marked genetic changes in declining North
Sea cod (Gadus morhua). 2003. Hutchinson, W. F., C. van Oosterhout, S. I. Rogers and G. R.
Carvalho. Proceedings of the Royal Society of London (B) 270:2125-2132.
cod population off the English Yorkshire coast (Flamborough Head)
fluctuated over a five-fold range between 1954 and 1998, and now has a
somewhat different genetic identity than when it started. Microsatellite
data were obtained from preserved otoliths covering the whole period. The
number of distinct alleles, considered to be the most sensitive measure of
diversity change, fell about 25% and then went back up again. "Furthermore, estimates of genetic differentiation (FST and
RST) showed a significant divergence between 1998 and earlier samples.
Data are consistent with a period of prolonged genetic drift, accompanied
by a replacement of the Flamborough Head population through an increased
effective migration rate that occurred during a period of high
exploitation and appreciable demographic and phenotypic change."
Cod is one of a group of
species in which the effective population size, which determines the rate
of drift, may be 5 or 6 orders of magnitude higher than the census size
(Jan 2003 #385, Aug 2003 #423). As a result of all this, the Flamborough
Head population disappeared as a distinctive genetic population then
re-emerged as a different one. The population size continues to fall. firstname.lastname@example.org
Heterozygous salmon grow faster and mature earlier
heterozygosity, date of first feeding and life history strategy in
Atlantic salmon. 2003. McCarthy, I. D., J. A. Sánchez and G.
Blanco. Journal of Fish Biology 62:341-357.
in this experimental study which were more heterozygous than the average started
feeding earlier (owing to more rapid embryonic development) and grew
faster than less heterozygous fish. Furthermore, "a significantly
higher proportion adopted the early freshwater maturation (age 0+ years,
male fish) or early migrant (age 1+ years, mainly female fish) strategies
compared to late first feeding Atlantic salmon". Age and size at maturation are of great interest both for
aquaculture and conservation of local populations at risk of extinction.
The authors explain their
observations using a threshold model, in which a developmental commitment
to early maturation is made late in the summer by fish that are relatively
large and on a fast-growth trajectory. The authors refrain from
speculating on the nature of the causal relationship between
heterozygosity and growth. See Jan 2002 #276 for a paper which discusses
the superior fitness of heterozygous trout. email@example.com
Wild and domesticated shrimp respond differently to different diet
Effect of a
size-based selection program on blood metabolites and immune response of
Litopenaeus vannamei juveniles fed different dietary carbohydrate. 2004.
Pascual, C., L. Arena, G. Cuzon, G. Gaxiola, G. Taboada, M. Valenzuela and
C. Rosas. Aquaculture 230:405-416.
hasn't been nearly enough work on the interaction between genetics and
diet in aquaculture; in particular we know practically nothing about the
way selection for fast growth might affect dietary requirements. It
certainly has an effect in other domestic animals and plants where,
generally speaking, the superior growth rate of selected genotypes is only
realized in superior nutritional environments.
This paper reports a
study of the effect of high carbohydrate (44%) and low carbohydrate diets
(3%) on lactate, protein other blood metabolites and hemocyte levels in
the shrimp Litopenaeus vannamei. (Dietary protein levels were 30% and 66%
respectively). The metabolic variables are indicators of immunocompetence
as well as growth. The carbohydrate effect was very different in wild and
domesticated shrimp. "Wild shrimp showed a direct relation between
dietary CHO [carbohydrate] and lactate, protein and hemocyte levels indicating that dietary CHO was
used for protein synthesis via transamination pathways." However, in
shrimp that had been domesticated (and selected) for 6 generations, the
metabolic indicator variables were lower in the high carbohydrate diet.
"These results demonstrate that during size-based breeding programs
other metabolic process than CHO catabolism can be selected. The
incapacity of shrimp to use dietary CHO [to produce protein, including immunoproteins and peptides] could limit protein reduction of diets and limit the efforts of the shrimp
industry to be ecologically and environmentally profitable." firstname.lastname@example.org
Farmed fish and their hybrids are inferior to wild salmon
and potential extinction of wild populations of Atlantic salmon, Salmo
salar, as a result of interactions with escaped farm salmon. 2003. McGinnity, P., P. Prodöhl, A. Ferguson, R.
Hynes, N. Ó Maoiléidigh, N. Baker, D. Cotter et al. Proceedings Royal
Society of London (B) 270:2443-2450.
is a careful and thorough study of the fitness of Irish farmed salmon
(originally a Norwegian stock) and native Irish salmon, in an Irish river.
Pure wild, pure cultivated, F1 hybrids and their F2 offspring and F1
backcrosses were evaluated for growth, survival and homing behaviour.
Survival and homing were worse in the farmed fish, and in all the types of
hybrids, than in the wild fish. The wild fish grew more slowly, however,
and the authors predict that size-dependent competition might cause
introgression of inferior farmed genes into the wild population. "[The authors] demonstrate that interaction of farm with wild salmon results in lowered
fitness, with repeated escapes causing cumulative fitness depression and
potentially an extinction vortex in vulnerable populations." See Jun 2001 #210 for extinction vortex, See Nov 2000 #130, Nov
2001 #260, Feb 2002 #287 for other papers which report reduced fitness in
wild/farm salmonid hybrids. But see Aug 2003 #416 for evidence of genetic
swamping possibly without accompanying loss of natural fitness.
F2 hybrids in this paper (offspring of hybrids mated among themselves) are
particularly interesting, because although it is rarely studied, reduced
performance in this generation can be a signal of outbreeding depression
(e.g. May 2003 #400) and/or breakdown of co-adapted sets of alleles during
recombination (these are not quite the same phenomenon). The authors
invoke coadaptation to explain the very low survival of F2 hybrid eggs.
However, there are some difficulties in believing that there is anything
more here than additive gene effects. In particular, if this coadaptation
does reflect the evolutionary divergence of aquacultural populations from
populations exposed to natural selection, it is odd that its effects are
seen only at the earliest developmental stage (pre-eyespot) when
emergence, early feeding, predator avoidance, agonistic interaction,
handling stress, site imprinting, homing behavior, appetite, feeding
latency, satiation, mate choice, fecundity and spawning behaviour - the components
of domestication selection people worry about - are somewhat irrelevant. The data show no sign of any F2 hybrid
inferiority which only begins to be expressed later in life, i.e. in
behavioral or other traits which affect survival from swim-up through to
smolt. Marine survival data for the F2 hybrids were not available, but
eyed-egg-to-smolt survival was not inferior and is probably much higher in
F2 hybrids than in wild fish.
If breakdown of
co-adaptation is indeed the cause of early embryo mortality it makes more
sense (to me) to ascribe it to ancient, river-specific differences rather
than to the recent selective effects of aquaculture. By extension, the
inferiority of these farmed and hybrid fish may be due to their
"Norwegian-ness", as much as to their "farmed-ness".
Discovering the cause of the F2 inferiority is important in the context of
strategies for re-introducing fish into extirpated rivers, genetic rescue
of remnant populations (May 2000 #51, Aug 2002 #341,May 2003 #400) etc. as
well as for containment issues in aquaculture. email@example.com
Genetic map for Clarias
genetic map of walking catfish (Clarias macrocephalus). 2004. Poompuang, S. and U. Na-Nakorn. Aquaculture 232:195-203.
authors have located 134 AFLP marker loci on 31 linkage groups. The
average spacing is 17 cM which makes it a useful framework for further
linkage mapping and QTL marking in this important aquacultural species. supawadee.p.@ku.ac.th
Sea-ranched trout are less involved in social interactions
Growth and social
interactions of wild and sea-ranched brown trout and their hybrids. 2003. Petersson, E. and T. Järvi. Journal of
Fish Biology 63:673-686.
laboratory study of wild, sea ranched (domesticated) and hybrid trout
found several traits that differ among the groups. Firstly, the ranched
trout grew somewhat faster. Secondly, the wild trout were in general more
aggressive. Thirdly, the results for hybrids were sensitive to which way
the hybridization was made, i.e. whether the wild parent was male or
female. An interesting multivariate framework for analysing behavioral
variables is developed in the paper.
The experiment was
designed to try to break the feedback loop in which animals which are
initially faster-growing (for any reason) become socially dominant owing
to their larger size, and then exploit their dominance to maintain their
superior growth rate. It was predicted long ago that in a well-managed aquacultural environment, playing social dominance mind-games is not an
evolutionarily stable strategy. If food is provided "fairly" in
a way that does not reward competitive fish with more food, then fish
which engage in energy-wasting aggression and/or lose their appetites when
they spot someone bigger than themselves will have a growth disadvantage.
If the aquaculturalist selects breeders from among the larger animals then
there should be an evolutionary trend towards "uninvolved"
phenotypes with reduced agonistic behavior. Something of the sort may have
happened here. See other wild domesticated comparisons by the same
authors: Sep 2001 #234 physiological response to stress, Aug 2003 #416
introgression of farmed into wild populations. firstname.lastname@example.org
A breeding plan for captive populations
inbreeding by managing genetic contributions across generations. 2003. Sánchez, L., P. Bijma and J. A.
Woolliams. Genetics 164:1589-1595.
equal numbers of males and females and producing two offspring per pair
still seems to be the best way to minimize inbreeding and loss of genetic
diversity in a controlled population. But what if it is impossible or
un-economic to breed equal numbers of both sexes? The current consensus
strategy (based on early work by Gowe et al., modified a few years ago by
Jinliang Wang) is that each sire should be replaced by one of its sons and
each dam by one of its daughters, with the exception that the dams which
produce the sons have no other offspring and should be replaced by
daughters of other dams. The Gowe-Wang strategy does somewhat increase the
variance of female reproductive success, however.
By addressing this
problem the authors of this paper show that inbreeding can be further
decreased. Their breeding strategy is too involved to be summarized here
but is well explained and diagramed in the paper. With 2 females per male
a randomly mated population (analogous to the haphazardly mated
populations of aquaculture) accumulates inbreeding twice as
fast as in their system. With an infinite number of females per male the
rate of inbreeding is 50% higher in a randomly mated population than in the
controlled breeding scheme proposed here.
See Dec 2001 #270 on
minimizing coancestry in early generations of a breeding program, Nov 2001
#261 for a general review of inbreeding-avoidance strategies. email@example.com
Sorting out the origins of hybrid populations
estimation of admixture proportions from genetic data. 2003. Wang, J. Genetics:747-765.
The situation envisaged here is an ancestral population
into two populations. These evolve separately for a while, then mix and
generate a hybrid population. Some time after the hybridization, samples
are take from the parental and hybrid populations, all three of which are
assumed to evolve in isolation except for the one-time hybridization
event. The problem is to estimate (a) the relative contribution of the
parental populations to the hybrid and (b) the amount of drift that has
occurred in each population at various points in the above scenario.
Obviously this is an important problem both for genetic conservation and
aquaculture -- sometimes even important in a forensic context.
The author discusses
various previous attempts to solve it, which have generally ignored the
effects of sampling errors and the drift of the parental populations. (See June 2002 #329.)
The new maximum likelihood method is presented and shown to be
considerably less biased and more robust to violations of the assumptions.
"The proposed likelihood method also has features such as relatively
low computational requirement compared with previous ones, flexibility for
admixture models, and marker types. In particular, it allows for missing
data from a contributing parental population." Software (entitled
LEADMIX) for performing the analysis can be downloaded free from http://www.zoo.cam.ac.uk/ioz/software.htm. firstname.lastname@example.org