[Paleopsych] is evolutionary change stockpiled?

[HowlBloom at aol.com]

There's a lot of material to back Greg up on "cryptic evolution"--evolution 
of the genome that takes place in hiding, not revealing itself in changes of 
the body of a creature.  There's also a lot to back him up in his notion of 
endogenous retroviruses--retroviruses packaged as part of the genome, then used by 
the genome as domesticated transport animals when the time is ripe.

And there's quite a bit to back up Joel's suspicion that the genetic shuttles 
of endogenous retroviruses and the hidden products of genetic research and 
development are tucked away in that horribly mislabeled stuff called junk dna.  
Here's more than you ever wanted to read on the topic.  Howard

http://news.bmn.com/news/story?day=010705&story=1, downloaded 7/6/01
 
  - 5 July 2001  Today's News Stories   News Archive When three steps forward 
is one step back  4 July 2001 17:00 GMT by Henry Nicholls, BioMedNet News 
Research published tomorrow further enhances Lewis Carroll's reputation as a 
closet evolutionary biologist by revealing, in an exceptional analysis according 
to some specialists, how genetic evolution can fail to keep up with a changing 
environment. Such "cryptic evolution", so called because the  evolving 
genotype is masked by an apparently unresponsive  phenotype, could be widespread in 
nature, says the Finnish  researcher who led the work.  The analysis focuses on 
a 20-year study of an isolated bird  population, reports Juha Merilä, senior 
researcher in the  department of ecology and systematics at the University of  
Helsinki. Collared flycatchers, Ficedula albicollis, on the  Swedish island 
of Gotland have evolved genes to increase their  body mass as the birds' 
environment has deteriorated, but they  are losing weight. "Quantitative genetic 
theory predicts that the relative body  mass of flycatcher offspring, which is a 
heritable trait under  positive directional selection, should increase over 
time, but  the relative mass at fledging has actually decreased," Merilä  told 
BioMedNet News. "Our results suggest that if today's flycatcher chicks were to  
experience a similar environment as the ones that lived in the  early 1980s, 
they would be much fatter than they are today,"  he said. "I would not be 
surprised if this [cryptic evolution] turned out  to be common," he added. "We 
should realize ... that similarity  in character state in time or space does not 
mean that  evolution has not occurred. A lot of evolution might be of this  
cryptic nature and we will keep on overlooking it unless we  focus more on 
similarities, rather than exclusively on  dissimilarities in character state," 
warned Merilä. "To my knowledge, this is the first time we have managed to  
demonstrate occurrence of cryptic genetic evolution over a  relatively short period 
of time in the wild," he said. The work impresses Peter Boag, professor of 
biology at  Queen's University in Ontario. "The really unique feature of  this 
study is that rarely has anyone collected sufficient data  from a real world, 
wild vertebrate population to allow a  believable dissection of this complex web 
of interactions,"  noted Boag. Merilä readily drew a parallel between his 
findings and the Red  Queen Hypothesis, which originates from Carroll's Through 
the  Looking Glass. "To my mind, the Red Queen metaphor is a  fascinating and 
an intuitive way of thinking about evolution," he  acknowledged. Leigh Van 
Valen, now professor of ecology and evolution at the  University of Chicago, 
famously drew on Carroll's fantasy tale,  and in particular the Red Queen's advice 
to Alice that "it takes  all the running you can do to keep in the same 
place", as a  metaphor for evolution. In 1973, he proposed that in a  changing 
environment, organisms must evolve just to maintain  their fitness. The hypothesis 
is most commonly cast in terms of two  organisms, such as the co-evolution 
between a parasite and its  host. As the parasite evolves novel ways of 
exploiting its host,  selection favours the host that evolves novel ways of defending  
itself against the parasite. Over an evolutionary timescale,  both parasite 
and host will have evolved and yet their  relationship might not have changed - 
neither will appear to be  any more successful at outwitting the other. 
However, in an interview with BioMedNet News, Van Valen  pointed out that "the Red 
Queen's Hypothesis can easily apply  to abiotically caused deterioration, which 
isn't usually  realized," and he agreed that Merilä's flycatchers seem to be  
subject to the paradox of the Red Queen. "The [flycatchers'] response to 
selection isn't enough to  prevent the population from deteriorating," he noted. 
"All the  running [the flycatchers] can do isn't enough to keep [them] in  the 
same place... It's pretty persuasive and fascinating  [research]," he said. 
Merilä speculates that a large-scale climatic trend could  underlie the 
worsening environment that the flycatchers are  experiencing. "Increased spring 
temperatures have led to  increasingly poor synchronization between the hatching 
date of  caterpillars and the date of bud-burst of the oak trees on which  they 
feed," he writes in this week's issue of Nature, published  tomorrow. This is 
bad news for the flycatchers, notes Merilä, because  caterpillars are the main 
source of food for growing nestlings.  And it raises the evolutionarily 
interesting question of "how far  can [the flycatchers] lag behind before they have 
to give up the  race?" Merilä concluded: "This strengthens my belief that 
long-term  population studies can be immensely valuable for both  evolutionary and 
environmental biologists, especially now that  we seem to be entering into an 
era of rapid environmental  changes caused by anthropogenic activities... 
These studies  can be a valuable resource in the future." Send us your feedback.  
 Printer ready version   E-mail article to a friend  See also:   Warmer 
springs disrupt the   synchrony of oak and winter moth   phenology.   [MEDLINE]   
Visser ME, Holleman LJ   Proc R Soc Lond B Biol Sci 2001 Feb   7 268:1464 
289-94   Parasites, predators and the Red   Queen   [News and Comment]   Koen 
Martens and Isa Schön   Trends in Ecology & Evolution,   2000, 15:10:392-393  In 
Search of the Red Queen   [Comment]   M.E.J. Woolhouse and J.P. Webster   
Parasitology Today, 2000,   16:12:506-508  In Search of the Red Queen: A   Response  
 [Letters]   Curtis M. Lively and Mark F.   Dybdahl   Parasitology Today, 
2000,   16:12:508  Heritable variation and evolution   under favourable and 
unfavourable   conditions   [Review]   Ary A. Hoffmann and Juha Merilä   Trends in 
Ecology & Evolution,   1999, 14:3:96-101   Related links on other sites:   The 
Red Queen: Sex and the   Evolution of Human Nature   by Matt Ridley   
Paperback - June 1995)   Amazon.com   Printer ready version   E-mail article to a 
friend  Today's News Stories  News Archive  
­­­­­­­­­­­­­­­­­­­
­­­­­­­­­­­­­­­­­­­05 July 2001  Nature 412, 76 - 79 (2001) © Macmillan 
Publishers Ltd. Cryptic evolution in a wild bird population J. MERILÄ*, L. E. B. 
KRUUK† & B. C. SHELDON‡§ * Department of Population Biology, Evolutionary 
Biology Centre, Uppsala University, Norbyvägen 18d, SE-752 36 Uppsala, Sweden † 
Institute of Cell, Animal and Population Biology, University of Edinburgh, 
Edinburgh EH9 3JT, UK ‡ Department of Zoology, University of Oxford, South Parks 
Road, Oxford OX1 3PS, UK § Department of Animal Ecology, Evolutionary Biology 
Centre, Uppsala University, Norbyvägen 18d, SE-752 36 Uppsala, Sweden  
Correspondence and requests for materials should be addressed to J.M. (e-mail: 
juha.merila at ebc.uu.se). Microevolution is expected to be commonplace, yet there are few 
thoroughly documented cases of microevolution in wild populations1, 2. In 
contrast, it is often observed that apparently heritable traits under strong and 
consistent directional selection fail to show the expected evolutionary 
response3, 4. One explanation proposed for this paradox is that a genetic response 
to selection may be masked by opposing changes in the environment5, 6. We used 
data from a 20-year study of collared flycatchers (Ficedula albicollis) to 
explore selection on, and evolution of, a heritable trait: relative body weight 
at fledging ('condition'). Despite consistent positive directional selection, 
on both the phenotypic and the additive genetic component (breeding values, 
estimated from an animal model) of condition, the mean phenotypic value of this 
trait in the population has declined, rather than increased, over time. Here we 
show that, despite this decline, the mean breeding value for condition has 
increased over time. The mismatch between response to selection at the levels of 
genotype and phenotype can be explained by environmental deterioration, 
concealing underlying evolution. This form of cryptic evolution may be common in 
natural environments.  If selection acts consistently on a heritable trait in a 
population, it should, all else being equal, induce a permanent change in the 
distribution of that trait7. The frequent lack of expected evolutionary change 
in heritable traits under directional selection in the wild has therefore 
puzzled evolutionary biologists for some time. Explanations proposed to account 
for this paradox include: inflated estimates of heritability owing to 
environmental covariance between relatives7, spatially and temporally varying selection 
pressures8, negative genetic correlations between different components of 
fitness8, and selection restricted to the environmental component of the 
phenotype3, 4. Another possibility is that a genetic response to selection does in 
fact occur, but is masked by opposing changes in the environment5, 6. However, to 
date, these alternatives have been subjected to very little empirical 
scrutiny8.  In many passerine bird species, relative body mass (the condition index) 
is an important predictor of the survival of fledglings: relatively heavier 
nestlings are more likely to survive to become breeding adults9-11. This is also 
true for juvenile survival in other taxa, such as reptiles12 and mammals13. 
In the collared flycatcher, quantitative genetic analyses using traditional 
methods suggest a significant additive genetic component to variation in the body 
condition index14. Mixed model analysis of variance using data for 17,717 
offspring in 3,836 breeding attempts, from a long-term study of this species on 
the island of Gotland, Sweden, confirms this finding, revealing a narrow-sense 
heritability of 0.30 (standard error, s.e. = 0.03; ref. 15). Analyses of 
survival selection show that there is significant positive directional selection on 
condition, such that the survivors are, on average, 0.23 (s.e. = 0.02; P < 
0.001) standard deviations above the population mean (Fig. 1a; ref. 15). In some 
years (6 out of 17), there is also significant stabilizing selection acting 
on condition, but this is both weaker and less consistent than the directional 
selection (Fig. 1b). Given that the condition index is heritable and under 
positive directional selection, we would expect the mean in this population to be 
evolving towards higher values. However, in contrast to this expectation, the 
mean condition in the population decreased significantly between 1981 and 
1999 (linear regression of annual means: b = -0.036, s.e. = 0.015, t15 = 2.35, P 
= 0.032; Fig. 2a; generalized linear mixed model (GLMM) of individual values, 
controlling for family structure and non-independence of observations from the 
same year: b = -0.035, s.e. = 0.003, t16,057 = 10.25, P < 0.001).  Figure 1 
Patterns of natural selection on condition  index of nestling collared 
flycatchers from 1981 to  1998. Full legend   High resolution image and legend (46k) 
Figure 2 Changes in condition index over time in the collared  flycatcher 
population from 1981 to 1999. Full legend   High resolution image and legend (46k) 
One plausible explanation for the lack of response to selection is that it is 
predominantly the non-heritable, or environmental, component of the condition 
index that determines survival3, 4, such that natural selection does not act 
on the genetic component of variation in condition. A role for environmental 
variation in natural selection is suggested by the observation that selection 
tends to be strongest in years when the mean condition is lowest (linear 
regression: b = -0.315, s.e. = 0.079, t15 = 4.24; P < 0.001; Fig. 1c). However, a 
direct test is to calculate selection on estimated breeding values, or the 
expected effect of the genes that an individual passes on to its offspring, which 
can be derived from pedigree information7. This analysis shows that selection 
acts directly on breeding values (standardized selection differential, S = 0.14, 
s.e. = 0.02, P < 0.001), not only on environmental deviations15. Furthermore, 
there is no evidence that a response to selection on condition would be 
constrained by negative genetic correlations with other fitness components. Both 
individual life-span (LSP) and lifetime reproductive success (LRS) are 
positively correlated with the breeding values for condition (GLMM: LSP, 2(1) = 9.88, P 
= 0.002; LRS, 2(1) = 21.42, P < 0.001; Fig. 3), and the genetic correlations 
between condition and LSP and between condition and LRS were 0.009 (s.e. = 
0.151) and -0.066 (s.e. =" 0.265), respectively: neither of these correlations 
was significantly different from zero.  Figure 3 Associations between key life 
history traits and estimated  breeding values (EBVs) for condition. Full legend 
  High resolution image and legend (58k) An alternative explanation for the 
apparent paradox "the absence of any evolutionary change despite significant 
directional selection on a heritable trait—lies in the possibility of change in 
environmental conditions over the study period5, 6. This explanation runs 
parallel to that suggested to account for the apparent lack of genetic 
differentiation across environmental gradients when such differentiation is expected—a 
phenomenon referred to as countergradient variation16 (Fig. 4a). 
Countergradient variation is defined as a negative covariance between the environmental and 
genetic influences on a given trait across some environmental gradient, and it 
can effectively conceal genetic differentiation when the environmental 
influence is sufficiently strong16. In the context of the current study the 
countergradient hypothesis would predict that, at the genotypic level, there should be 
a positive correlation between year of the study and condition index. Using 
estimated breeding values we found that the mean estimated breeding value had 
indeed increased over the course of the study (linear regression of annual 
means: b = 0.0022, s.e. = 0.0009, t15 = 2.38, P = 0.030; GLMM of individual 
values: b = 0.0023, s.e. = 0.0008, t16,057 = 2.70, P = 0.007; Fig. 2b). Hence, 
despite the negative trend at the phenotypic level (Fig. 2a), at the level of the 
genotype the population mean condition index has increased over time.  Figure 4 
Environmental deterioration over time.  Full legend   High resolution image 
and legend (41k) The estimated microevolutionary change has presumably been 
concealed by an increasingly negative influence of environmental conditions on 
the condition index (Fig. 4a), which has caused the phenotypic decline. The 
intensity of selection on the condition has increased with time (linear 
regression: b = 0.015, s.e. = 0.007, t17 = 1.99, P = 0.06; Fig. 1d), and fledging 
success has decreased with time (Fig. 4b; linear regression: b = -0.011, s.e. = 
0.003, t18 = 3.19, P < 0.005). Both relationships are indicative of environmental 
deterioration. A plausible agent explaining this deterioration is the 
large-scale climatic trend that has reduced the caterpillar food supplys" "the main 
food of growing nestlings—over the last few decades17. Increased spring 
temperatures have led to increasingly poor synchronization between the hatching date 
of caterpillars and the date of bud-burst of the oak trees on which they feed. 
Estimates of the lag between caterpillar hatching date and oak bud-burst date 
from a Dutch study17 were positively correlated with the annual mean 
condition index (coefficient of correlation r = 0.613, test statistic z17 = 2.76, P = 
0.0057; Fig. 4c), tarsus length (r = 0.621, z17 = 2.89, P = 0.0021) and 
fledging success (r = 0.531, z17 = 2.82, P = 0.0049; Fig. 4d) of collared 
flycatchers on Gotland. Because the degree of synchrony between caterpillar emergence 
and bud-burst dates is driven by large-scale climatic phenomena17, such 
correlations can be expected to occur across continental scales. Increased intra- and 
interspecific competition, both of which lower condition in this18, 19 and 
other bird populations20 are other potential, but perhaps less likely, 
explanations for the decline in reproductive success and condition observed in this 
study.  In conclusion, in accordance with data from studies of spatial genetic 
differentiation16, our results show that microevolutionary transitions at the 
genotypic level need not necessarily be manifested at the phenotypic level16, and 
that an apparent lack of evolutionary response in a heritable trait subject 
to directional natural selection can be understood in terms of the environment 
masking genotypic evolution, rather than selection on environmental deviations 
only3. Alternative explanations for the lack of selection response (that is, 
biased heritability estimates, negative genetic correlations between the focal 
trait and other components of fitness, reversed direction of selection on 
later life stages) could be excluded on the basis of detailed analysis using new 
methods. To this end, our results concur with the view21, 22 that many 
evolutionary transitions may consist of changes not visible at the level of the 
phenotype.  Methods The data The material for this study was collected between 1980 
and 1999 from a nest-box-breeding collared flycatcher population inhabiting 
the island of Gotland, off the Swedish east coast in the Baltic sea. All 
breeding attempts were monitored from the date of egg-laying until all nestlings had 
fledged. When 12 days old, nestlings were measured for tarsus length with 
digital calipers (to nearest 0.1 mm), weighed with a Pesola spring balance (to 
nearest 0.1 g) and marked with individually numbered aluminium rings. At the 
same time, their parents were captured and their identity was checked (see refs 
14 and 15 for more information on collection procedures). Condition index was 
estimated as the residuals from a linear regression of body mass at fledging on 
tarsus length (see refs 10 and 14 for details and analysis of linearity of 
this relationship). Data were available for 4,888 breeding attempts involving 
23,336 individuals. Because the sexes do not differ in growth patterns or 
condition at fledging23, data on both sexes were analysed together (with one 
exception: see below). Breeding attempts subject to manipulative experiments were 
excluded from the analyses.  Quantitative genetic analyses Heritability of 
condition and individual breeding values were estimated through a mixed model 
restricted maximum likelihood (REML) estimation procedure using the software 
packages VCE24 and PEST25. An individual 'animal model' was fitted, in which an 
individual's phenotypic value of condition was broken down into components of 
additive genetic value and other random and fixed effects7, 26. The area of the 
study site and the year were included as random effects to account for spatial 
and temporal heterogeneity in environmental effects on phenotype. Nest-box 
identity was also fitted as a random effect to account for further 
common-environment effects specific to the individual brood; this term will incorporate any 
non-genetic maternal effects. The only fixed effect in the model was a 
population mean. The narrow-sense heritability (h2) was estimated as the ratio of the 
additive genetic variance (VA) to the total phenotypic variance (VP): h2 = 
VA/VP. Best linear unbiased predictors (BLUP) of individual breeding values were 
quantified from pedigree information using REML estimates of variance 
components, with the software package PEST25. BLUP estimates of breeding values (EBVs) 
are unbiased even in populations under selection, or exhibiting assortative 
mating, and estimates from different generations will reflect changes in 
additive genetic effects resulting from selection, genetic drift or inbreeding7. With 
an annual breeding population size in excess of 1,500 pairs, the occurrence 
of genetic drift in this population is unlikely. Calculation of inbreeding 
coefficients (IBCs) revealed that only 0.5% of pairings resulted in individuals 
with an IBC greater than 0, and there was no evidence for between-year 
heterogeneity in IBCs (Kruskal–Wallis H18 = 15.15, P = 0.65; estimated using Pedigree 
Viewer, available from http://www-personal.une.edu.au/~bkinghor/pedigree.htm). 
Changes in EBVs across generations can therefore be taken as evidence of a 
response to selection, or 'genetic trend'27, 28. Genetic correlations were 
estimated from a multivariate animal model analysis of fledgling condition, 
life-span (LSP; in years) and lifetime reproductive success (LRS; defined as the 
number of offspring recruited into the breeding population). Genetic correlation 
analyses were necessarily restricted to individuals surviving to adulthood; area 
and year were included as random effects, and sex (known for individuals 
recaptured as adults) as a fixed effect.  Selection analyses Estimates of survival 
selection on phenotypic and estimated breeding values of condition index were 
based on recapture data under the assumption that nestlings not returning to 
the study area in subsequent years had died. As many of the individuals 
recruit to the population at the age of two years, the survival analyses were 
restricted to the period of 1981–1998. Standardized directional (S) and quadratic 
(c2) selection differentials were estimated by linear regression of relative 
fitness on standardized (zero mean, unit variance) phenotypic or breeding values 
of the condition index using standard methods29. Statistical significance of 
the selection differentials was estimated with logistic regression29. 
Associations between individual LSP or LRS and EBVs for condition were tested using 
GLMMs with negative binomial error structure, using the procedure IRREML in 
Genstat30. Nest of origin, year and area were included as random effects in the 
model, to account for repeated measures. The significance of the fixed effect of 
condition breeding value as a predictor of LSP or LRS was assessed by the Wald 
statistic, distributed as 2(1) (ref. 30).  Received 26 February 2001;accepted 
14 May 2001  References  1.  Grant, P. R. & Grant, B. R. Predicting 
microevolutionary responses to directional  selection on heritable variation. Evolution 
49, 241-251 (1995). 2.  Reznick, D. N., Shaw, F. H., Rodd, F. H. & Shaw, R. 
G. Evaluation of the rate of  evolution in a natural population of guppies. 
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M. & Arnold, S. J. Directional selection and the evolution of  breeding date 
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Gustafsson, L. & Lundberg, A. Phenotypic selection on heritable size  traits: 
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F., Taylor, P. D., Frances, C. M. & Rockwell, R. F. Directional selection and  
clutch size in birds. Am. Nat. 136, 261-267 (1990). 6.  Frank, S. A. & 
Slatkin, M. Fisher's fundamental theorem of natural selection. Trends  Ecol. Evol. 7, 
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Traits (Sinauer,  Sunderland, Massachusetts, 1998). 8.  Roff, D. A. 
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& Smith, J. N. Determinants and consequences of nestling condition in  song 
sparrows. J. Anim. Ecol. 60, 995-1008 (1991).  10.  Lindén, M., Gustafsson, L. & 
Pärt, T. Selection of fledging mass in the collared  flycatcher and the great 
tit. Ecology 73, 336-343 (1992).  11.  Both, C., Visser, M. E. & Verboven, N. 
Density-dependent recruitment rates in great  tits: the importance of being 
heavier. Proc. R. Soc. Lond. B 266, 465-469  (1999). | Article |  12.  Sorci, 
G. & Clobert, J. Natural selection on hatching body size and mass in two  
environments in the common lizard (Lacerta vivipara). Evol. Ecol. Res. 1, 303-316  
(1999).  13.  Boltnev, A. I., York, A. E. & Antonelis, G. A. Northern fur seal 
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Zool. 76, 843-854 (1998). | Article |  14.  Merilä, J. Genetic variation in 
offspring condition--an experiment. Funct. Ecol. 10,  465-474 (1996).  15.  
Merilä, J., Kruuk, L. E. B. & Sheldon, B. C. Natural selection on the genetical  
component of body condition in a wild bird population. J. Evol. Biol. 
(submitted).  16.  Conover, D. O. & Schultz, E. T. Phenotypic similarity and the 
evolutionary significance  of countergradient variation. Trends Ecol. Evol. 10, 
248-252 (1995).  17.  Visser, M. E. & Holleman, L. J. M. Warmer springs disrupt the 
synchrony of oak and  winter moth phenology. Proc. R. Soc. Lond. B 268, 
289-294 (2001). | Article | PubMed |  18.  Gustafsson, L. Inter- and intraspecific 
competition for nest holes in a population of the  collared flycatcher Ficedula 
albicollis. Ibis 130, 11-16 (1988).  19.  Doligez, B., Danchin, E., Clobert, 
J. & Gustafsson, L. The use of conspecific  reproductive success for breeding 
habitat selection in a non-colonial, hole-nesting  species, the collared 
flycatcher. J. Anim. Ecol. 68, 1193-1206 (2000). | Article |  20.  Alatalo, R. V. & 
Lundberg, A. Density-dependence in breeding success of the pied  flycatcher 
(Ficedula hypoleuca). J. Anim. Ecol. 53, 969-978 (1984).  21.  Lewontin, R. C. 
Adaptation. Sci. Am. 239, 212-230 (1978). | PubMed |  22.  Gilchrist, A. S. & 
Partridge, L. A comparison of the genetic basis of wing size  divergence in 
three parallel body size clines of Drosophila melanogaster. Genetics 153,  
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Ellegren, H. Gender and environmental  sensitivity in nestling collared 
flycatchers. Ecology 79, 1939-1948 (1998).  24.  Groeneveld, E. REML VCE, a Multivariate 
Multi-Model Restricted Maximum Likelihood  (Co)Variance Component Estimation 
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Behaviour, Federal Research Center of Agriculture  (FAL), Mariensee, Germany, 
1995). http://www.tzv.fal.de/institut/genetik/pub/eg/vce/manual/manual.html  
25.  Groeneveld, E., Kovac, M., Wang, T. L. & Fernando, R. L. Computing 
algorithms in a  general purpose BLUP package for multivariate prediction and 
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maximum-likelihood to estimate variance components for animal  models with several 
random effects using a derivative-free algorithm. Genet. Selection  Evol. 21, 
317-340 (1989).  27.  Blair, H. T. & Pollak, E. J. Estimation of genetic trend 
in a selected population with and  without the use of a control population. J. 
Anim. Sci. 58, 878-886 (1984). | PubMed |  28.  Southwood, O. I. & Kennedy, B. 
W. Genetic and environmental trends for litter size in  swine. J. Anim. Sci. 
69, 3177-3182 (1991). | PubMed |  29.  Merilä, J., Sheldon, B. C. & Ellegren, 
H. Antagonistic natural selection revealed by  molecular sex identification of 
nestling collared flycatchers. Mol. Ecol. 6, 1167-1175  (1997).  30.  
Genstat, 1998. Genstat 5, Release 4.1 (Lawes Agricultural Trust, IACR, Rothamsted,  
1998). Acknowledgements. We thank I. P. F. Owens, A. J. van Noordwijk, B. Walsh 
and D. A. Roff for comments on the manuscript, M. Visser for data on 
caterpillars and oaks, and the numerous people who have helped in collecting the data 
in the course of the study, in particular L. Gustafsson. Our research was 
supported by the Swedish Natural Science Research Council, the Nordic Academy for 
the Advanced Study (J.M.) and by Royal Society University Research Fellowships 
to B.C.S. and L.E.B.K.  Nature © Macmillan Publishers Ltd 2001 Registered No. 
785998 England.
_Retrieved from the World Wide WebJune 13, 2003
http://www.sciencemag.org/cgi/content/full/300/5623/1246?maxtoshow=&HITS=10&hi
ts=10&RESULTFORMAT=&fulltext=ALU+transposons&searchid=1055484085580_14300&stor
ed_search=&FIRSTINDEX=0&fdate=10/1/1995&tdate=6/30/2003
GENOMICS:
Not Junk After All   Wojciech Makalowski   Science 2003 May 23; 300: 
1246-1247. (in Perspectives) 
Not Junk After All Wojciech Makalowski*  From bacteria to mammals, the DNA 
content of genomes has increased by about three orders of magnitude in just 3 
billion years of evolution (1). Early DNA association studies showed that the 
human genome is full of repeated segments, such as Alu elements, that are 
repeated hundreds of thousands of times (2). The vast majority of a mammalian genome 
does not code for proteins. So, the question is, "Why do we need so much 
DNA?" Most researchers have assumed that repetitive DNA elements do not have any 
function: They are simply useless, selfish DNA sequences that proliferate in 
our genome, making as many copies as possible. The late Sozumu Ohno coined the 
term "junk DNA" to describe these repetitive elements. On page 1288 of this 
issue, Lev-Maor and colleagues (3) take junk DNA to new heights with their 
analysis of how Alu elements in the introns of human genes end up in the coding 
exons, and in so doing influence evolution.  Although catchy, the term "junk DNA" 
for many years repelled mainstream researchers from studying noncoding DNA. 
Who, except a small number of genomic clochards, would like to dig through 
genomic garbage? However, in science as in normal life, there are some clochards 
who, at the risk of being ridiculed, explore unpopular territories. Because of 
them, the view of junk DNA, especially repetitive elements, began to change in 
the early 1990s. Now, more and more biologists regard repetitive elements as a 
genomic treasure (4, 5). Genomes are dynamic entities: New functional 
elements appear and old ones become extinct. It appears that transposable elements 
are not useless DNA. They interact with the surrounding genomic environment and 
increase the ability of the organism to evolve. They do this by serving as 
recombination hotspots, and providing a mechanism for genomic shuffling and a 
source of "ready-to-use" motifs for new transcriptional regulatory elements, 
polyadenylation signals, and protein-coding sequences. The last of these is 
especially exciting because it has a direct influence on protein evolution.  More 
than a decade ago, Mitchell et al. showed that a point mutation in an Alu 
element residing in the third intron of the ornithine aminotransferase gene 
activated a cryptic splice site, and consequently led to the introduction of a partial 
Alu element into an open reading frame (6). The in-frame stop codon carried 
by the Alu element resulted in a truncated protein and ornithine 
aminotransferase deficiency. This discovery led to the hypothesis that a similar mechanism 
may result in fast evolutionary changes in protein structure and increased 
protein variability (7). Several genome-wide investigations have shown that all 
types of mobile elements in all vertebrate genomes can be used in this way. The 
unsolved mystery is how a genome adapts to the drastic changes conferred on a 
protein by the insertion of a mobile element into the coding region of its 
gene. Lev-Maor and co-workers and a second group now demonstrate how this process 
takes place without disturbing the function of the original protein (see the 
figure) (3, 8).  Figure 1 Junk DNA caught in the act. Two ways in which a 
repetitive DNA element, such as an Alu element, can be incorporated into the 
coding region of a gene without destroying the gene's function. (Top) A TE-cassette 
is inserted into the mRNA as an alternative exon. (Bottom) Insertion of a 
TE-cassette is preceded by a gene duplication. In both cases, the genome gains 
two forms of the mRNA transcript--one with and one without the TE-cassette.  
Last year, Sorek et al. (9) noticed that about 5% of alternatively spliced 
internal exons in the human genome originate in an Alu sequence. Interestingly, 
because Alu elements are primate specific, these exons must be primate or human 
specific as well as much younger than other exons in a gene. Additionally, they 
noticed that the vast majority of "Alu exons" are alternatively spliced (that 
is, there is always another messenger RNA without the Alu element in the 
coding region). They concluded that "Alu elements have the evolutionary potential 
to enhance the coding capacity and regulatory versatility of the genome without 
compromising its integrity" (9).  In their new work, this group now shows how 
alternative splicing of Alu exons is regulated (3). It is well established 
that the precise selection of the 3' splice site depends on the distance between 
the branch point site (BPS) and the AG dinucleotide downstream of the BPS. 
The optimal distance between the BPS and the AG dinucleotide is relatively 
narrow (19 to 23 nucleotides). Interestingly, if there is another AG dinucleotide 
closer to the BPS, it will be recognized by a spliceosome even if a second AG 
located more optimally is used in the transesterification reaction (10). A 
splicing factor, hSlu7, is required to facilitate recognition of the correct AG. 
Thus, the correct selection of the 3' splice site is an interplay between AG 
dinucleotides and certain splicing factors.  It is even more tricky to maintain 
the delicate balance of signals that cause an exon to be spliced 
alternatively--you make one mistake (a point mutation) and either a splicing signal becomes 
too strong and an exon is spliced constitutively, or the signal becomes too 
weak and an exon is skipped. Lev-Maor and colleagues (3) performed a series of 
experiments to identify an ideal sequence signal surrounding the 3' splice 
site within the Alu element that kept the Alu element alternatively spliced. It 
appears that in addition to the distance between two AG dinucleotides, a 
nucleotide immediately upstream of proximal AG is also important. Hence, a proximal 
GAG sequence serves as a signal weak enough to create an alternatively spliced 
Alu exon. Any mutation of a proximal GAG in the first position results in a 
constitutive Alu exon. This is an important observation because most of the 
more than 1 million Alu elements populating the human genome contain such a 
potential 3' splice site. Of these, 238,000 are located within introns of 
protein-coding genes, and each one can become an exon. Unfortunately, most mutations 
will lead to abnormal proteins and are likely to result in disease. Yet a small 
number may create an evolutionary novelty, and nature's "alternative splicing 
approach" guarantees that such a novelty may be tested while the original 
protein stays intact.  Another way to exploit an evolutionary novelty without 
disturbing the function of the original protein is gene duplication (see the 
figure). Gene duplication is one of the major ways in which organisms can generate 
new genes (11). After a gene duplication, one copy maintains its original 
function whereas the other is free to evolve and can be used for "nature's 
experiments." Usually, this is accomplished through point mutations and the whole 
process is very slow. However, recycling some modules that already exist in a 
genome (for example, in transposons) can speed up the natural mutagenesis process 
tremendously. Several years ago, Iwashita and colleagues discovered a bovine 
gene containing a piece of a transposable element (called a TE-cassette) in 
the middle of its open reading frame (12). This cassette contributes a whole new 
domain to the bovine BCNT protein, namely an endonuclease domain native to 
the ruminant retrotransposable element-1 (RTE-1). Interestingly, the human and 
mouse homologs of bovine BCNT lack the endonuclease domain but instead contain 
a different one at their carboxyl terminus. This raised two questions: When 
did the BCNT protein acquire the endonuclease domain, and how did the bovine 
genome manage such a drastic rearrangement of BCNT without losing its fitness? 
Iwashita et al. give the answers to both questions in their new study (8). They 
discovered another copy of the bovine bcnt gene that resembles mammalian bcnt 
homologs (also called CFDP1) just six kilobases downstream of the gene with 
the TE-cassette. Both copies of the gene are apparently expressed and both 
proteins are functional. Phylogenetic analysis suggests that shortly after gene 
duplication in the ruminant lineage, one of the copies acquired an endonuclease 
domain from an RTE-1 retrotransposon. Not surprisingly, this gene undergoes 
accelerated evolution.  The reports by Lev-Maor et al. and Iwashita and 
colleagues describe different ways in which genes can be rapidly rearranged and acquire 
evolutionary novelty through the use of so-called junk DNA. These discoveries 
wouldn't be so exciting if they didn't show how genomes achieve this without 
disturbing an original protein. To quote an old Polish proverb: "A wolf is 
sated and a lamb survived." These two papers demonstrate that repetitive elements 
are not useless junk DNA but rather are important, integral components of 
eukaryotic genomes. Risking personification of biological processes, we can say 
that evolution is too wise to waste this valuable information. Therefore, 
repetitive DNA should be called not junk DNA but a genomic scrapyard, because it is 
a reservoir of ready-to-use segments for nature's evolutionary experiments 
(13).  References 1. M. Nei, Nature 221, 40 (1969) [Medline].  2. R. Britten, D. 
Kohne, Science 161, 529 (1968) [Medline].  3. G. Lev-Maor, R. Sorek, N. 
Shomron, G. Ast, Science 300, 1288 (2003).  4. J. Brosius, Science 251, 753 (1991) 
[Medline].  5. R. Nowak, Science 263, 608 (1994) [Medline].  6. G. A. Mitchell 
et al., Proc. Natl. Acad. Sci. U.S.A. 88, 815 (1991) [Medline].  7. W. 
Makalowski, G. A. Mitchell, D. Labuda, Trends Genet. 10, 188 (1994) [Medline].  8. 
S. Iwashita et al., Mol. Biol. Evol., in press.  9. R. Sorek, G. Ast, D. Graur, 
Genome Res. 12, 1060 (2002) [Medline]. 10. K. Chua, R. Reed, Mol. Cell. Biol. 
21, 1509 (2001) [Medline]. 11. S. Ohno, Evolution by Gene Duplication 
(Springer-Verlag, New York, 1970). 12. T. Nobukuni et al., J. Biol. Chem. 272, 2801 
(1997) [Medline]. 13. W. Makalowski, Gene 259, 61 (2000) [Medline]. The author 
is at the Institute of Molecular Evolutionary Genetics and Department of 
Biology, Pennsylvania State University, PA 16802, USA. E-mail: wojtek at psu.edu 
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Spliced Exon: 3' Splice-Site Selection in Alu Exons Galit Lev-Maor, Rotem Sorek, 
Noam Shomron, and Gil Ast Science 2003 300: 1288-1291. (in Reports) [Abstract] 
[Full Text] Volume 300, Number 5623, Issue of 23 May 2003, pp. 1246-1247. 
Copyright © 2003 by The American Association for the Advancement of Science. All 
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Retrieved December 16, 2002, from the World Wide Web 
http://darwin.bio.uci.edu/~faculty/villarreal/new1/erv-placental.html
The following is a detailed and referenced document.  The Viruses That Make 
Us:  A Role For Endogenous Retrovirus In The Evolution Of Placental Species  by 
Luis P. Villarreal Chromosome evolution, higher order and parasitic elements. 
With the accumulation of genomic sequence data, certain unexplained patterns 
of genome evolution have begun to emerge. One striking observation is the 
general tendency of genomes of higher organisms to evolve an ever decreasing gene 
density with higher order. For example, E. Coli has a gene density of about 2 
Kb per gene, Drosophila 4 Kb per gene and mammalian about 30 Kb per gene. Much 
of the decreased density is due to the increase in the accumulation of 
non-coding or 'parasitic DNA' elements, such as type one and two transposons. 
Current evolutionary theory does not adequately account for this observation (81). 
In addition mammals appear to have retained the presence of at least some 
copies of non-defective 'genomic retroviruses', such as intercysternal A-type 
particles (IAP's) or endogenous retroviruses (ERVs), (51,85). It is currently 
difficult to account for the selective pressure that retains these genomic viruses, 
since they often lack similarity to existing free autonomous retroviruses. It 
is widely accepted that viral agents act a negative selecting force on their 
host. However, viral agents have very high mutation and adaption rates. This 
character led Salvador Luria to speculate early on that perhaps viruses 
contribute to host evolution (52). There is now sufficient evidence to suggest that 
horizontally transmitted agents and gene sets allow the rapid adaption of 
various living systems, including bacteria, yeast, drosophila and hymenoptera. 
'Pathogenic islands' are contiguous regions of DNA that contain gene sets in 
bacteria that appear to be horizontally acquired and can exist as either prophage, 
episomes or genomic sequences (21). These pathogenic islands appear to account 
for much of the rapid adaptability in bacteria. Transposons of Drosophila 
appear to require horizontal transmission in order to be maintained during 
evolution and appear to have been the underlying mechanism of hybrid dysgenesis 
(10). The parasitioid wasp species (hymenoptera) maintain genomic polydnaviruses 
in most species which are highly produced into non-replicating viral forms 
during egg development and subsequently suppress host larval immunity making them 
essential for egg survival (47,74). Thus horizontally transmitted genetic 
elements are common in the genomes of all species. The mammalian chromosome 
presents an especially interesting case of accumulation of 'parasitic' DNA. All 
placental species have unique LINE elements present at very high abundance as well 
as other related and even more abundant elements, such as the SINES or 
primate specific alu elements (see (70) for references). Yet there appears to be no 
common progenitor to these elements. All these elements appear to be products 
of reverse transcription of cellular RNA's however, there is no explanation 
for the conservation to RT activity in mammals. Although endogenous retroviruses 
are found in most organisms prior to mammalian radiation, the levels of these 
genomic agents is relatively low in non-mammals and the nature of retroposons 
seems distinct form that in mammalian. Mammalian LINES, for example lack a 
precise 5' end, have no poly-A 3' end, and lack RT coding regions that are 
characteristic of all LINE elements as opposed to avian or other retroposon 
elements of vertebrates that do not have these features. Why are mammalian 
(eutherian) chromosomes especially so full of these RT derived agents? What selects for 
their generation or retention? A genomic retrovirus: essential for placentals? 
In a proposal published in 1997, I raised the issue of endogenous retrovirus 
and proposed that these viruses are essential to the biology of Eutherians. 
Viviparous mammals confront an immunological dilemma in that mammals which have 
highly adaptive immune systems fail to recognize their own allogenic embryos 
(58). The relationship of mammalian mother to her fetus resembles that of a 
parasite and host in that the fetus 'parasite' must be able to suppress the 
immune response of the 'host' mother in order to survive. As viviparous mammals are 
also noteworthy for having genomes that are highly infected with endogenous 
retroviruses and as retroviruses are generally immunosuppressive, the possible 
participation of endogenous retroviruses in the immunosuppression by the 
embryo was then considered. In addition, it was considered if such endogenous 
viruses might be more broadly involved in the evolution of their host and the 
resulting host genome that now appear to have many derivatives (such 
retrotransposons and as LINE elements) of such genomic viruses. This grant application seeks 
support to do an experimental evaluation in a mouse model of the proposed 
involvement of endogenous retroviruses in the immunologically escape by the 
embryo in the mother. I argue that endogenous retrovirus is hence essential for the 
biology of non-egg laying placental mammals. This study could provide 
evidence of the biological function of endogenous retroviruses and also address the 
broader issues concerning the possible contribution of genomic virus to host 
genome evolution. The dilemma of viviparous mammals and their allogeneic 
embryos. This mammalian dilemma was clearly stated by Medawar in the early 1950's, 
see (31,50). Since then, this dilemma has remained one of the most vexing and 
persisting problems in immunology. An array of models have since been proposed 
attempting to explain this situation. These include a limited embryonic 
expression and presentation of MHC class I or class II antigen ((88) or expression of 
alternative MHC, HLA I-G, (40), or a high hydrocortisone hormonal suppression 
of immunity, and more recently the possible role of Fas L embryonic 
expression in ablating T-cell recognition of the embryo (66). All of these models, 
though with some support, have significant problems. Inflammatory reactions, which 
appear to be involved in embryo rejection (see below) would not be checked by 
low MHC expression. Lowered MHC I expression would also be expected to elicit 
a natural killer cell response, which appears to be important in embryo 
implantation (41), although the human embryo specific alternative MHC gene, HLA-IG, 
could substitute for MHC I to negatively regulate NK activity. Up regulated 
expression of Class I MHC by interferon does not allow CTL killing of 
trophoblasts suggesting that trophoblast actively inhibit CTL killing (for references, 
see (26)). Also, humans with deficient beta-2 microglobulin do not express 
HLA-IG yet the fetus comes to term indicating HLA-IG is not essential for 
implantation (James Cross, personal communication). In addition, other species, such 
as mouse have no analogue of the HLA-IG antigen, which suggest this antigen 
cannot be a general solution to the immunological dilemma of viviparous species. 
Fas null mice, although displaying defects in peripheral clonal immune 
selection, allow implantation of embryos (1). General immune suppression, such as 
hydrocortisone cannot explain the relatively normal immune response in pregnant 
mothers to many agents or elevated level of TH2 reactive cells (which are 
important for mucosal macroparasite elimination) seen in pregnant woman, see T. 
Mossman, (49). Also, the glucocorticoid effect may be mediated via the p15E-like 
gene of endogenous retrovirus (20). In addition, it is interesting to note 
that autoimmunity, such as rheumatoid arthritis can often abate during pregnancy 
suggesting an altered immunity that appears not mediated via hormones 
(Fackelman, Science News 144:260). Most effective immune reactions appear to be of a 
rather local nature. Therefore local suppression seems a likely way to 
regulate embryo immune recognition. Although TH1 reactivity in pregnancy is weak, the 
TH2 response, which is important for inflammatory like reactions, is not 
decreased and is possibly enhanced (T. Mossman). Neither the MHC model, nor the 
Fas-Fas ligand model can account to the failure to initiate an inflammatory 
reaction or NK activity against the embryo (activated NK cells can reject 
xenografts (41)) The Role of Mucosal Uterine Macrophages or NK cells Embryo 
implantation occurs in the mucosal epithelial tissues of the uterus. Like most mucosal 
surfaces, the uterus has a high abundance of macrophages (37,70) and NK cells 
(41). Once activated, these cells should respond vigorously to parasites or 
allogeneic tissues and reject xenografts. The regulation of these cells and their 
subsequent inflammatory reaction and induction of the adaptive immune 
response involves IL-1 beta, IL-6, TGF beta-1, TNF-alpha, CSF-1 (26,88). The uterus 
appears to present an immunologically tolerant site as grafts into the uterus 
of pregnant rats have prolonged survival relative to other locations, see (5) 
for review. Macrophages are central to the initiation of innate and subsequent 
adaptive immune responses (18). Although most macrophages can act as 
immunostimulatory cells, evidence suggest that uterine macrophages can make 
immunosuppressive molecules. For example, despite MHC II display, uterine macrophages 
don't present antigens to T-cells (44). Other results suggest that uterine 
macrophages can contribute to embryo loss. Preterm mouse delivery is associated with 
high levels of macrophage derived IL-1-beta, IL-6, TNF- a . High rates of 
early embryo loss can be associated with the specific mouse strains that are 
mated in that low rates of embryo loss can sometimes be seen with inbred 
crossings, whereas some outbred crossings can show higher embryo loss rates. For 
example, crosses between CBA/J X DBA/2 are prone to early embryo loss relative to 
inbred crosses which is enhanced by IFN induction (27). This breeding associated 
embryo loss is also linked with inflammation and iNO production by local 
decidual macrophages (27) as inhibition of macrophage iNO enhanced litter size. 
Macrophage iNO inactivates nearby macrophages and mediates immunosuppression in 
inflammation via bystander lymphocyte autocytotoxicity, suggesting a way to 
elicit immunosuppression. The Importance of Trophoblast Role in implantation. In 
the implanting embryo, trophoblasts are the first cells of the egg to 
differentiate. Following the loss of the zona pellucida shell, trophoblast 
differentiate into cytotrophoblast the finally into the fused syncytiotrophoblast that 
forms the cell layer that directly contacts the uterus and the mothers blood 
system. These trophoblasts are considered a part of uterine macrophage-cytokine 
network (26,88). Trophoblast resemble macrophages in many of the genes that 
they express. Uterine macrophage produced IL-1 which may play critical role 
during implantation (28). Trophoblasts protect inner cell mass from macrophage 
destruction (69). Trophoblast can be transplanted across mouse strain barriers 
without being rejected suggesting they have immunosuppressive activities (38). 
Also, trophoblasts have a very unique pattern of gene expression in that 
expression is restricted to paternal (androgenic) genes while inner cell mass 
express maternal genes (79). This is in stark contrast to other somatic tissues 
where mosaic expression is observed. With trophoblast gene expression being 
androgenic (79,80), it seems curious that X chromosome inactivation is also paternal 
in trophoblast, see Renfree (61) for references. It is interesting therefore 
to note that female mice are less able to kill tumors bearing paternal 
antigens then tumors bearing maternal antigens (T. Mossman, personal communication). 
Trophoblasts are intriguing in an evolutionary sense as well. Other 
non-viviparous mammals (marsupials, monotremes) completely lack the 
trophoblast-syncytiotrophoblast layer, see (59) for review. Unlike viviparous mammals, marsupial 
gestation is short (averaging several to 12 days), their eggs are yolk-filled 
resembling those of reptiles and marsupial eggs are surrounded by a maternal 
derived shell membrane which once lost allows only minimal maternal-fetal 
contact for a period of only several days. Most of marsupial egg incubation is 
outside of mothers body and birth is associated with local inflammatory events. 
Marsupials also lack hormonal control of uterus or other tissues (61). Given that 
the trophectoderm is the first mammalian egg cell type to differentiate and 
the relatively recent evolutionary development of this layer in mammals, early 
embryos of the viviparous mammal do not seem to recapitulate evolutionary 
history with respect to this first cell type. Thus the trophoblastic cells appear 
to be centrally involved in implantation and embryo immunomodulation. 
Trophoblast produced ERV's. Another rather unique feature of syncytiotrophoblasts is 
in their ability to produce a high quantity of endogenous retroviruses , see 
(85). This also appears to be a general characteristic of all placental mammals. 
The production of endogenous retroviruses in early mammalian embryos is a 
long standing and often repeated observation. Multiple detections of particles in 
normal human embryonic cells, especially basal surface of human placental 
syncytiotrophoblast tissue have been frequently reported as have similar particle 
production in old and new world primates placentas (for early review see 
(84)). Normal human placentas have measurable RT activity (56) and appear to 
express HERV env gene (45). Primary trophoblasts of rhesus monkeys also produce 
ERV's (77). Furthermore, the levels of mouse virus particle production can be as 
high as 105 per cell (60), which exceeds by far the capacity of most 
permissive cell culture systems for retrovirus production. In addition, these 
endogenous retrovirus particles are frequently made following induction in testicular 
teratocarcinoma which constitute a HERV (Human Endogenous Retrovirus) group, 
similar to C-type particle (85). In addition, antibody studies have established 
that CTL reactive to ERV proteins can be found in most pregnant woman as can 
immuno-precipitation reactivity to p28, p15 and p15E (for references see (85), 
p. 86-87). Interestingly, RD114 cross-reactive antibodies were significantly 
correlated with complications during pregnancy and with prior abortions and 
stillbirths (78). In humans, these trophectoderm expressed HERV's represent two 
large diverse multi copy families HERV-R and HERV-K., the latter is capable of 
expressing the env and p15E gene products in vaccinia vectors (83). Thus, 
endogenous retrovirus are mainly isolated from reproductive embryonic tissues but 
to a lesser extent from circulating lymphocytes or monocytes of some mouse 
strains (42). These viruses are highly suppressed in most somatic tissues 
probably due to DNA methylation, (see below). However, these viruses do not seem 
transmissible in usual sense of leading to productive infections. Nondefective 
endogenous retroviruses are conserved and expressed in trophoblast HERVs 
constitute about 0.6% of the human genome and appear more related to rodent viruses 
than any known human viruses. The great majority of these endogenous viruses are 
defective and deleted of various gene products, especially the env gene but 
also gag/pol. For an early review of the human endogenous retroviruses see 
(46). Initially, it was felt that there all copies of HERV's in the genome were 
defective, but it subsequently became clear that highly conserved non-defective 
copies also exist at low levels (see Urnovitz (85) table 6 , p.93 for refs.). 
For example, the HERV-K sequence of the human teratocarcinoma derived virus 
type (HTDV), is reported to be able to make retrovirus like particle and can 
express gag, pol and env genes via vectors (83). Also, ERV 3 can express env gene 
in embryonic placental tissues (45). Such reports may now explain the 
numerous early observations of being able to find viral particles in human tissues 
(13), (see (33) for early references). Although some HERV's are expressed in 
mammary tumors, the feline RD114, ERV-3, and HERV K10+ are all expressed in 
placental tissues. What then is the significance of nondefective ERVs and why is 
expression so common in embryos? There has developed a confusing system of 
nomenclature and corresponding phylogenetics of ERVs due to multiple names for 
similar viral sequences. In addition, sequences from several ERV's appear to be 
made up of mosaic elements such that different relationship will be apparent 
when different parts (e.g. gag/pol vs env) are analyzed as seen with HERV-K10+, 
which can add to confusion (85). A relatively clear system of nomenclature has 
been presented by Urnovitz and Murphy (85). They propose HERV's can be 
classified according to established non-defective endogenous viruses. For example, 
both the ERV-1 (with a deleted env region) and the single copy ERV-3 (which can p
lacentally express an intact env gene) are also called HERV-R (45) can be 
classified as ERV-3 derivatives. Accordingly, the defective HERV-K10 with deleted 
env, or the non-defective full length HERV-K10+ and the HERV K(C4), are thus 
related to HERV-K10+. In addition, RTLV-H, in which most copies are pol 
defective but is also expressed in embryonic tissues and also has an env gene (32), 
is present as a low copy nondefective copy; RTLV-Hp. Interestingly, this 
RTLV-Hp sequence appears to have been conserved phylogenetically (via neutral codon 
substitutions) and implies that it belongs to a functional and selected 
subclass of highly retained ERV's (89). This classification method allows clearer 
identification of highly conserved and intact ERVs. What could an ERV function 
be for the host cell? I (68) and Venables et al. in the Boyd group (8,86) have 
proposed that some of these HERV's may function during embryo implantation to 
help prevent immune recognition by the mother's immune system. Immunological 
activity of ERV (IAP) genes Most retroviruses appear to be generally 
immunosuppressive of the host immune system (for review see (25)). The 
immunosuppressive nature of retroviruses was first investigated in detail with feline leukemia 
virus of domestic cats (FeLV) and led to the identification of the CKS-17 
hydrophobic transmembrane domain of the env gene as an important immune 
modulator. This domain is present in the highly conserved p15E peptide which maintains 
the immunosuppressive character, for review see (30). A main effect of p15E is 
to inhibit T-cells via cytokine (TNF and IFN ) mediated processes (29) and 
can be elicited by synthetic or recombinant p15E (65,67). p15E also inhibits 
mononuclear phagocyte chemotaxis (85). Thus the env gene is a primary candidate 
of an ERV gene product that could modulate the mother's immune recognition, 
which fits well with its proposed role in syncytiotrophoblast expression. In 
addition, the ERV gag gene product may also be immuno-modulatory. The p70 (gag) of 
mouse IAP has been cloned and expressed and shown to be identical to IgE 
binding factor (IgE-BF) which is a regulator of B-cell ability to produce IgH 
(43,54). More recently, it has been reported that endogenous gag is Fv-1, 
an-Herv.L like endogenous virus which confers resistance to MLV tumors (7). Although 
some researchers disagree with the immunomodulatory role of p15E, an immune 
suppressing activity in culture assays has been clearly established. These 
supporting results seem sufficiently clear to warrant a serious investigation that 
both the env and gag gene products of ERV's may modulate immunity. ERV's and 
placental macrophages If non-defective ERV gene (env) products are indeed 
immuno-modulatory, we can now offer explanations for various other observations. For 
one, env expression should be highly selected for in the early embryo (hence 
the conserved single intact copy), but strongly counter selected for 
expression in ectopic sites which would render these genes inappropriately 
immunosuppressive. Therefore most transposed copies of ERV's would be expected to be under 
selection to lose the env gene, as is observed. Also, ERV expression is 
somatic tissue is generally highly repressed, also as expected from this model. In 
addition, it can be expected that the main target of ERV action would be the 
local immune cells of the uterus. A likely cell type to affect would be the 
uterine macrophages. Given the central role of innate immune modulators (18) and 
macrophages (2) in the induction of the acquired immune response, uterine 
macrophages and the cytokines they effect seems a likely candidate to target for 
embryo immune regulation. However, there is no evidence that ERV's are 
transmitted in a productive manner. We therefore might expect the trophectoderm 
derived ERV's act more like a replication defective recombinant retrovirus that is 
able to effect locally exposed cells, but not replicate and transmit to other 
cells (see (87). This would mean that these ERV's are essentially local acting 
agents. Thus a central unanswered question is what effect IAP producing 
trophoblasts have on nearby macrophages, especially with respect to a macrophage's 
role in innate and acquired immune function. Of some relevance to this issue 
are reports glucocorticoid mediates increased Mtv env (p15E) expression in 
P388D1 macrophage and T-like mouse line (20). Such cell systems could be used 
experimentally to examine possible role of env in immune modulation. One seemingly 
contradictory observation concerning the above proposal is that normal embryo 
development appears to occur in the presence of inhibitors of reverse 
transcriptase, AZT, such as in AZT treated HIV infected mothers which generally 
produce normal offspring. If the embryo produced ERV's are needed for immune 
modulation, it seems likely that embryo's would be immunologically rejected if RT 
inhibitors prevent the production of ERV's. However, early embryo development is 
severely affected by AZT, see (82). AZT will efficiently inhibit normal 
embryo's at post fertilization but preimplantation stages. AZT is toxic to early 
embryos at before blastocyst stage however, but it is not toxic at post 
blastocyst implantation stage (82). The possibility that embryos were being rejected by 
the mother's immune system was not examined in these studies. An additional 
consideration concerning the possible use of RT inhibitors is that because the 
ERV's are being produced in the trophectoderm from genomic copies of virus, RT 
inhibitors are not expected to inhibit trophectoderm produced ERV's as viral 
genomes are already integrated as DNA (88). Support for this comes from HIV 
studies showing that AZT did not inhibit HIV gene expression in infected 
placental trophoblasts. However, it might be predicted that local immune cells, such 
as uterine monocytes or macrophages, might not be properly 'reprogrammed' to 
immune nonrecognition by ERV's infection as the integration step in these cells 
would be inhibited. Once these macrophages were reprogrammed by ERV 
infection, their 'anergic' state could persist rendering them resistant to further RT 
inhibitors as long as the cells live, which is seldom known for these cell 
types. Clearly, this issue should be examined experimentally. IAPs and cancer IAP 
expression, although normally highly repressed, is often observed in various 
tumor tissues (14,15,90). If these ERVs are a normal host system of immune 
modulation as I have proposed, it could be expected that tumors would select for 
the expression of immuno-modulatory ERV or ERV gene products (such as p15E) in 
order to avoid immuno-surveillance. Early reports presented evidence that p15E 
is made in many human breast cancers (73). This suggest that tumor cells 
might also be used as an experimental system in which to examine this issue. In 
some tumors, there appears to be interesting converse links between IAP 
expression and tumor recognition. BL6 melanoma normally make high levels of IAP and do 
not express H-2kLd . IAP production can affect IgE production and is 
conversely is lost when MHC-I H-2kLd ,and H-2kLb but not H-2Dd H-2Ld is transfected 
into BL6 cells (48). Also, P15E-like proteins in serum, urine and tumor 
effusions of cancer patients suppress immune responses that can be reversed by 
anti-p15E antibody (71,73). ERV (IAP) genetics and implications for the functional 
subsets. Because human and mouse ERV's are present at about 900 copies per 
haploid genome, a genetic analysis would appear to present a daunting if not 
impossible task. For example, gene knockout experiments in mice, which have been so 
valuable at elucidating gene function, would seem not possible in the context 
of IAPs. However, intact env genes are sometimes present at much lower levels, 
and in some cases as single copies (ERV-3). It seems likely that this limited 
subset is the functional set that might be important. ERV-3 seems like a very 
good candidate that could provide immunosuppressive barrier between human 
mother and fetus as it has highly expressed env in syncytiotrophoblasts, 
expresses antigens that react to antibodies specific to the transmembrane domain 
(p15E-like), and is present as a complete, single copy sequence on chromosome 7, 
(Larsson, '97 NEED THIS) (86). Other good candidate human ERV's are the 
HERV-K(C4) and HERV-K which are also highly expressed in the placenta. Interestingly, 
Y human chromosome has lots (20) of different ERV's related to ERV3 (Kjellman, 
Sjogren, Widegren, '95, NEED THIS) which may code for potential HY antigens. 
However, what is really needed for experimental analysis is the mouse 
homologue to the human ERV-3. One possible functional homologue is the IAPE virus 
which like ERV-3, has an intact env sequence (62). In addition, this IAP env 
sequence appears to be expressed as a protein in NH15-CA2 cell lines suggesting a 
functional gene (62). The IAPE sequences, however, are complicated by the 
existence of about 200 copies/cell in mus musculus (63). But the IAPE-A locus seems 
complete and intact relative to the other IAPE's which lack gag or pol 
sequences and IAPE-A is present at lower levels. IAPE's are found in all lab strains 
(mostly Mus musculus domesticus derived) in variable and genetically unique 
levels that identify the strain (12), suggesting an unexplained link of 
inbreeding to IAPE variation. Some outbred strains, such as CE/J, had much lower 
levels of IAPE sequences, but maintain IAPE-A (75). These CE/J mice might offer a 
simpler genetic system to investigate the possible function of IAPs. Yet, 
mouse strains do not seem to vary much with respect to the very massive RNA levels 
(105 copies per cell) of early embryo expressed IAP (60). As IAPE-A is 
complete and it also codes for intact env sequence, this seems like a logical but 
untested candidate for possible trophectoderm expression. IAPE-Y is an IAPE-A so 
named because it has amplified on Y-chromosome. However, the Y-amplified head 
to tail copies are not found in all musculus species indicating that this 
amplification appears to be a recent evolutionary change (19). The repetitive 
head to tail Y-copies of IAPE are limited to only male Mus musculus domesticus 
and the asian Mus musculus molossinus and M. Musculus castaneus. The more 
distant Spanish Mus spretus lacked the repetitive copies on the Y chromosome, but 
conserved IAPE-A. MuRVY is genetically associated but distinct from IAPE, is 
also on Y and could represent a second class of trophectoderm expressed IAPs 
(17,19). Y condensation in most tissue (except testes Sertoli cells) probably 
limits expression of these IAP-Ys. However, IAPE-A expression, (also related to 
Hamster H-18 IAP (3)), although usually highly repressed in most tissues, may at 
times be expressed in some somatic (thymus) tissues of some mouse strains 
(42). Phylogenetic studies suggest that this env gene was under functional 
constrains not to evolve quickly, although the defective copies are evolving very 
rapidly. Thus IAPE-A seems like a good candidate for an ERV env gene involved in 
mouse embryo implantation. However, it has not previously been established 
that this env sequence is expressed in trophoblasts (see preliminary results 
below). The possible relevance of ES and EC cells. It has long been established 
that some testicular derived teratocarcinoma cells can differentiate from 
embryonal stem cells into several cell types (76). Of particular interest is the 
capacity of some EC lines to differentiate into trophectoderm. Treatment with 
10-3 M retinoic acid will differentiate some of these cells into parietal 
trophectoderm-like cells which will eventually develop structures resembling a 3.5 
day blastocyst. Thus this tissue resembles the extra-embryonic trophectoderm 
that is the proposed source of immunosuppressive ERV's. Along these lines, it 
has also long been established that differentiated (but not undifferentiated) 
mouse EC cells induces high levels of two distinct populations of IAPs (36). 
Thus at least by this parameter, EC cells my accurately model trophectoderm gene 
specific control. Other reports show IAP production in differentiated EC cells 
can be significantly reduced without affecting the ability of these cells to 
differentiate into trophectoderm. F9-EC cells containing integrated SV40 
sequences (F912-1 cells), resulted in IAP production that was significantly reduced 
after differentiation. In these cells, it appears that IAP expression is 
tightly linked to DNA methylation and that SV40 has affected methylation without 
affecting cell specific expression (34). EC cell differentiation has been well 
characterized and many expressed sequence tags have been catalogued (57). It 
should therefore be possible to accurately determine if the EC differentiation 
program is otherwise affected by SV40 T-Ag or other regulatory proteins. 
Historically, EC cells were also used to study cell specific replication by 
polyomavirus. This led to the development of enhancer variants of polyomavirus that 
had increased capacity to replicate in undifferentiated EC cells. Using the 
enhancer/origin from Py (PyF101), Gassmann et al. with P. Berg constructed a Py 
T-Ag expressing plasmid (PMGD20neo) that allowed for episomal selection in ES 
cells (9,24). This plasmid had the interesting capacity to be stably maintained 
as an episome in ES cells without integration. Some of the resulting ES cell 
lines could then be used to make mosaic mice that also maintained the Py 
plasmid. Thus it seems clear that the presence of Py T-Ag expressing DNA was not 
detrimental to the development of most normal mouse tissues. This plasmid could 
offer a very useful experimental tool for the genetic analysis of ES and EC 
cell function (see below). Another interesting use of EC and ES cells concerns 
their ability to grow into masses (tumor-like) in the more immunologically 
privileged site of the brain. Both ES and EC cells can be differentiated into 
trophectoderm containing embryoid bodies. These embryos will generally grow in 
various transplanted sites only with immunosuppression. However, following brain 
implantation of embryoid bodies, ES cells will grow rapidly into large masses 
(91). Implantation of 2-4 cell embryos, which lack trophectoderm, however, do 
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page, please contact Einstein at uci.edu  Last Updated 7/14/1999 

In a message dated 11/22/2004 8:43:11 PM Eastern Standard Time, 
ursus at earthlink.net writes:
It's a provocative idea, isn't it? Invisible mutations, occurring at the
metabolic level, in the "infrastructure," so to speak, but not manifesting
in large-scale phenotypic changes. 

However, I think it's also apparent that all organisms today have a set of
"grammatically correct" bauplan variations that can be called upon in
incremental (but not gradual) stages in response to environmental challenges
over perhaps hundreds or thousands of years in larger animals, and tens of
years in insects, and days or weeks in bacteria. 

The best recent example is the reoccurrence of wings in stick insects...

Best wishes!

Greg  

-----Original Message-----
From: paleopsych-bounces at paleopsych.org
[mailto:paleopsych-bounces at paleopsych.org] On Behalf Of Geraldine Reinhardt
Sent: Monday, November 22, 2004 5:32 PM
To: The new improved paleopsych list
Subject: Re: [Paleopsych] is evolutionary change stockpiled?

Could be.  Check with Greg Bear.

Gerry Reinhart-Waller
Independent Scholar
http://www.home.earthlink.net/~waluk

----- Original Message ----- 
From: "Steve Hovland" <shovland at mindspring.com>
To: "'The new improved paleopsych list'" 
<paleopsych at paleopsych.org>
Sent: Monday, November 22, 2004 4:15 PM
Subject: RE: [Paleopsych] is evolutionary change 
stockpiled?


> Is it possible that there are incremental changes
> in the environment that don't require an immediate
> outward response, but which do cause a series of
> "invisible" mutations which suddenly manifest when
> the environmental changes reach some triggering 
> level?
>
> Steve Hovland
> www.stevehovland.net
>
>
> -----Original Message-----
> From: HowlBloom at aol.com [SMTP:HowlBloom at aol.com]
> Sent: Monday, November 22, 2004 3:42 PM
> To: paleopsych at paleopsych.org
> Subject: [Paleopsych] is evolutionary change 
> stockpiled?
>
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----------
Howard Bloom
Author of The Lucifer Principle: A Scientific Expedition Into the Forces of 
History and Global Brain: The Evolution of Mass Mind From The Big Bang to the 
21st Century
Visiting Scholar-Graduate Psychology Department, New York University; Core 
Faculty Member, The Graduate Institute
www.howardbloom.net
www.bigbangtango.net
Founder: International Paleopsychology Project; founding board member: Epic 
of Evolution Society; founding board member, The Darwin Project; founder: The 
Big Bang Tango Media Lab; member: New York Academy of Sciences, American 
Association for the Advancement of Science, American Psychological Society, Academy 
of Political Science, Human Behavior and Evolution Society, International 
Society for Human Ethology; advisory board member: Youthactivism.org; executive 
editor -- New Paradigm book series.
For information on The International Paleopsychology Project, see: 
www.paleopsych.org
for two chapters from 
The Lucifer Principle: A Scientific Expedition Into the Forces of History, 
see www.howardbloom.net/lucifer
For information on Global Brain: The Evolution of Mass Mind from the Big Bang 
to the 21st Century, see www.howardbloom.net
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