The Evolutionary Context of Genomic Imprinting

The conventional Mendelian
model for diploid organisms assumes that the expression of an autosomal
allele within an individual should be invariant of its sex of origin,
that is, whether it is inherited from the father or the mother. 
This model is incorrect for a subset of alleles across many taxa, in
particular mammals.  In 1989 David Haig and Mark Westoby outlined
the evolutionary rationale for parent specific gene expression.¹ 
In 1992 paternal and maternal specific imprinting of the insulin growth
factor 2 and insulin growth factor 2 repressor loci (Igf2,

Igf2r) in mice confirmed their predictions.² Over the
last 15 years as many as 200 loci have been identified as being subject
to parental specific genomic imprinting.³  The mechanisms
involved are clear at the most basic level, the repression of gene expression
via epigenetic mechanisms such as methylation, but the details of the
molecular genetic processes are still relatively obscure and mysterious.⁴ 
But perhaps the larger question is why parental specific gene expression,
operationally the transformation of a locus to a haploid or monoallelic
expressive state, should occur on a particular subset of loci. 
Fundamentally this is an evolutionary question, and concurrently with
the proximate exploration of the molecular mechanisms there has grown
a theoretical body of work which explores the ultimate rationale of
the emergence of these peculiar molecular systems. 

What is the relevance of theory
to biology?  The examination of biological questions has traditionally
occurred on various methodological and organizational levels. 

Darwin's theory of evolution via natural selection upon heritable
variation was proposed without a viable genetic theory.  It was
40 years between the publication of The Origin of Species and
the emergence of modern genetics, and another 20 years before evolutionary
biology integrated the Mendelian framework.⁵  Of course,
this preceded the work of Francis Crick and James Watson on DNA, so
for a generation the Neo-Darwinian Modern Synthesis of evolutionary
biology and genetics existed without any understanding of the biochemical
nature of genes.  These historical precedents show that despite
a lack of understanding of mechanistic details, an evolutionary theoretical
program can be fruitful in laying the groundwork for future understanding
of a whole system, and a cogent set of predictions may serve as the
blueprint for a detailed line of work to elucidate proximate causes. 

Currently there are three primary
theoretical evolutionary explanations for the emergence of genomic imprinting,
the "Evolvability Hypothesis," the "Ovarian Time Bomb Hypothesis"
and the "Kinship Theory."  As the Kinship Theory seems the
most well supported and thoroughly developed project, I will focus on
it through most of this paper and only introduce the general outlines
of the first two theories.   

The Evolvability Hypothesis
is a model which proposes that genomic imprinting is a mode of transmission
which allows genetic variation to be maintained within the population.⁶ 
The rough logic is similar to the reasoning behind the maintenance of
sex in complex diploid organisms, the long term fitness of populations
which maintain genetic variation by shielding alleles of suboptimal
fitness from selection by masking their expression should be greater
than populations which allow full biallelic expression and so purge
less fit alleles from the population.  There are problems with
this model in the details.  First, one must consider that because
parental specific gene expression alternates between active and repressed
states when inherited from the mother or father, there is little guarantee
of long term masking from selection for a given allele.  For example,
if one posits that a maternal allele is silent, the probability of that
allele being masked from selection via maternal transmission a given
number of generations is simply 0.5 to the power of generations under
consideration.  In other words, the number of generations one may
expect to be silenced is rather short, and though this model assumes
environmental and other selective pressures change rapidly so as to
render suboptimal alleles more optimal over time, such drastic variation
seem unrealistic.  Additionally, there is the reality that for
recessive alleles, which are normally masked by a dominant allele in
a diploid organism, genomic imprinting's haploid expression pattern
would increase its chances of being exposed to selection.  In a
conventional panmictic scenario the vast majority of low frequency recessives
would be in heterozygote genotypes where they would be masked, while
in the context of genomic imprinting one could expect that monoallelic
expression would result in these recessives being exposed to selection
without the "protection" of a dominant copy of the given gene. 

In fact, these recessives offer up a much more plausible way of maintaining
genetic variation within a population without recourse to genomic imprinting. 
Additionally, there is the issue that the proponents of the Evolvability
Hypothesis make reference to the fitness of groups, which is very difficult
to model and justify in most evolutionary genetic systems.  The
ubiquity of sex suggests that some long term fitness implication of
groups might be at play, but the relative paucity of loci which exhibit
genomic imprinting seems to weigh against an appeal to such theoretically
tendentious paradigms.  Finally, in regards to the empirical data
the Evolvability Hypothesis has no easy explanations for why such a
general fitness advantage (i.e., increased genetic variability) would
only manifest on a minuscule fraction of the genome, exhibit a patchy
phylogenetic distribution (e.g., be more prominent in mammalian lineage)
or predict why paternally inherited copies would be more likely to be
over-expressed in relation to maternal copies.  In short, such
a general solution resting upon shaky theoretical foundations seems
unwarranted.⁷ 

The Ovarian Time Bomb Hypothesis
is a more specific model.  Its rationale is that paternal specific
expression is necessary as a failsafe against premature oocyte development
and subsequent invasion maternal tissue by trophoblasts.⁸ 
This hypothesis explains why there is a tendency for maternal copies
to be repressed and paternal copies to be expressed, and the genes which
are evolved in trophoblast development do seem to be under imprinting
control.  Nevertheless this hypothesis' problem is the inverse
of the Evolvability Hypothesis in that it is highly specific. 

Loci not involved in trophoblast development are assumed to have been
imprinted by byproduct mechanisms, perhaps due to their proximity to
imprinted loci. Additionally, the hypothesis assumes that ovarian tissue
would have higher metastatic potentional when this is not assured. 
It maybe that male germ cells, sperm, are simply more malignant and
so stronger selection works against them.  Inactivation of maternal
alleles could then have arisen for another reason, while relaxed selection
would have allowed the emergence of relatively benign teratomas of oocytes. 
Perhaps most importantly, there seems to be little difference in imprinting
between mammalian lineages with invasive placenta (i.e., subject to
trophoblast invasions and tumors) and non-invasive placenta. Finally,
the monoallelic imprinting of most somatic tissues must be assumed to
be a byproduct of selection against ovarian tumors, but there is strong
evidence that loss of heterozygosity is a major selective force which
might reduce fitness of the organism with many cells which exhibit such
monoallelic expression.  In sum, though the Ovarian Time Bomb Hypothesis
is not illogical or vague, its specific and precise predictions are
met and exceeded to such an extent that it seems unable to account
for the wider scope of genomic imprinting.⁹ 

The third and most well developed
hypothesis is the Kinship Theory, also termed "Conflict Theory,"
which is really an extension of the general paradigm of inclusive fitness
elucidated by W.D. Hamilton in his famous series of papers in 1964 which
outlined the general logic by which altruism could evolve through selection
on the level of genes.¹⁰  The logic is straightforward. 

Consider an individual.  This individual is diploid, and so carries
two copies of each gene, alleles, inherited from their mother and father. 
Similarly, their mother and father also carry two copies of each gene,
from their own mothers and fathers. The probability of a given allele,
one of two copies, being passed to the next generation is ½. 
An individual is identical by descent on ½ of their alleles from either
parent. Similarly, the offspring of a given individual is identical
by descent on ½ of their alleles.  As grandparents of an individual
are at one remove, one is expected to be identical by descent on about
¼ of their alleles from any given grandparent.  This is an expectation,
you have no guarantee which grandparent's allele you will inherit
and sampling variance will likely result in differences of genetic contribution
from those in your lineage who one would expect would contribute equitable
proportions to your genome.  In other words, the probability of
identity by descent on most lines of relationship when comparing given
loci between two individuals is an expectation only. Nevertheless, evolution
works over many generations and across populations, so even though siblings
are only expected to be, not necessarily going to be on the sequence
level, identical by descent ½ of the time, evolutionarily speaking
one assumes this as a deterministic truth as the sampling variance tends
to decrease inversely to the square root of the number sampled. 

The probability of two alleles
on a given locus across generations or between individuals defines the
"coefficient of relatedness" between them, r.  Because
of the haplodiploid nature of hymenoptera genetics Hamilton showed in
his 1964 paper how eusociality was a highly plausible arrangement for
this taxon because the coefficient of relatedness between sisters, 0.75,
was greater than that between mothers and their offspring, 0.5. 

The logic can be illustrated by a "thought experiment."  Consider
an allele, A, which encodes a drive to be altruistic to your
kin in relation to the coefficient of relatedness, r.  If
this allele programs one to come to the aid of someone who is near kin
then it is "aiding" itself because its presence in said near kin
would be directly proportional to r.  In contrast, a selfish
allele S, would encode a strategy of selfishness to one and all. 
Of course some of the times that the allele A

drove one to help someone who was related to you would be aiding
S, but what truly counts is the average over time.  If you
aided the other individuals a great deal, then the cost to yourself
might be compensated by the benefit to them.  Why would a benefit
to them be relevant?  They carry the allele A
as well! Formally this is depicted by "Hamilton's Rule," a behavior
is favored if B x r > C, where B

denotes the "benefit to the other," r
is the coefficient of relatedness between the other and oneself and
C is the cost to yourself.  If one aids someone whose r
to oneself is 0.5 so as to increase that individual's fitness by greater
than a factor of 2, then even a reduction of one's own fitness to
zero is justified as (2 + x) x
0.5 > 1, 1 being the cost to oneself. 

Of course there are many simplifying
assumptions here.  Inbreeding necessarily increases r, and
of course there is extremely high sequence level identity of human genomes
(for that matter, there is ~98% sequence level identity between chimpanzees
and human beings) so the key is relative relatedness and a focus on
recent identity by descent as opposed to identity by state or ancestral
descent.  Nevertheless, the basic logic seems to explain a great
deal of the behavior in the animal, and even human, world. But how
is this relevant to genomic imprinting?  The key is to go beyond
one of the implicit simplifying assumptions above, the invariant nature
of the parents in the models, or, more precisely, the invariant nature
of the father.  In a situation where the father varies a great
deal, as is common in many mammalian species, the r
across maternally and paternally inherited genes in the offspring, from
now on denoted madumnal and

padumnal alleles, differs.  While madumnal
alleles still exhibit the canonical cross-sib r
of 0.5, the padumnal alleles can be expected to be less than
0.5.  The reason is two fold, first, in many mammals mating pairs
last only for one breeding season, so siblings are likely to have different
fathers. Additionally, in many species which birth litters there is
multiple-paternity of the siblings because of multiple matings in a
season.  This results in an expectation of r

being lower across padumnal
alleles, and so all things being equal Hamilton's Rule now differs
between the maternally and paternally inherited alleles in some cases.¹¹ 
An extreme case is between half-siblings who are known to differ in
paternity.  On their madumnal
alleles their r is 0.5, on their padumnal
alleles their r is 0, averaging together for the canonical coefficient
of relatedness of 0.25.  In species where paternity certainty is
not known the padumnal r

will be proportional to the expectation of paternity identity across
siblings.¹² 

This difference between
r results in a host of conflicts across genetic loci.  The
key for genomic imprinting is that mammals are characterized by relatively
high obligate maternal investment and vivaparity results in a basal
metabolic cost to the mother for any given offspring.  In contrast
there is a wide range of paternal investment and certainty.  The
initial work in genomic imprinting derived from the genetic conflicts
that occurred between the fetus and the mother in mammalian species.¹³ 
And to some extent the mother-offspring tug of war for resources is
still the crux of the matter.  In a situation where pair-bonds
are minimal or transient the cost to the father, and ergo, the padumnal

alleles, of reductions in future fitness of the mother, ergo, the
madumnal alleles, is minimal.  Therefore there is a strong
incentive for padumnal alleles to induce aggressive acquisition
of resources of offspring and transfer of fitness from the mother and
to offspring.  In contrast, the madumnal
alleles are shared between mother and offspring at the value of r
0.5, and between the offspring and future offspring to the value of
0.5, so there is a strong disincentive for the madumnal

alleles of the offspring from incurring a catastrophic fitness cost
to the mother.  In terms of how this plays out on the molecular
level the loci which should exhibit genomic imprinting would be those
focused on early growth of the fetus and resource allocation to the
offspring.  This is the general trend one sees in the mouse model,
Igf2 the first gene to be implicated in genomic imprinting in mice
is a growth factor.¹⁴  Because of the costs of monoallelic
expression, vulnerability to loss of heterozygosity and haploinsufficiency,
only loci which effect such highly fitness relevant phenotypes should
be targeted by genomic imprinting as otherwise the costs to both
madumnal and padumnal alleles would be too great.  In
this fashion the narrow scope of imprinting's genomic impact, as well
as its functional biases, are accounted for. 

One of the predictions the
Kinship Theory of genomic imprinting, which is validated, is that there
will be a strong bias toward padumnal
expression in an attempt to trigger and induce growth and resource monopolization
in its "selfish" drive toward increasing its own fitness irrelevant
to the cost of the unrelated mother.  But critics have pointed
out that in many circumstances where genomic imprinting should not be
operative bias still occurs.  The reason is that in cases where
the probability of paternity is very certain, operationally close to
100%, the madumnal and padumnal alleles have the same
interests.  Additionally, in such "monandrous" circumstances
there is often concomitant male parental investment, so excessive offspring
demands incur a cost upon future padumnal

alleles.  It seems than an implication of Kinship theory would
be that madumnal and padumnal
alleles would "agree" upon expression levels and exhibit no asymmetry,
but this is not so. But this is a fallacious prediction, for what the
Kinship Theory predicts is that the total sum dosage should now be agreed
upon between the two parental copies, the means by which the dosage
occurs (i.e., the proportional contributed via expression from each
copy) is irrelevant.¹⁵ 

To flesh out this phenomenon
one must backtrack and consider the evolutionary trajectory via which
imprinting occurs. The hypothesis conjectures that over time the
padumnal allele increases dosage while the madumnal
allele decreases dosage in a species where genetic conflict occurs.
Over time the madumnal allele reaches zero expression, that is,
it is silenced. At this point the padumnal

allele would be assumed to win by default as it would increase dosage
to the appropriate level to optimize its own fitness (one assumes to
over-expression might be deleterious for a variety of reasons). 
One must remember that it seems likely that other repressor madumnal
alleles would begin to interfere with the unchecked padumnal
allele (e.g., Igf2r in most mammals repressing Igf2),
but nevertheless, the final evolutionary end state should be alternative
expression states for the maternal and paternal origin copies in the
offspring.  If the life history of the species alters for some
reason from a competitive polyandrous to a stable monandrous norm, then
the rational for the asymmetry disappears, and the two parental alleles
would agree upon dosage. One might imagine that the padumnal

allele would at this point begin to reduce its expression levels toward
a lower state to increase its own future fitness because it is now tied
to the madumnal allele, but this dose not imply that the madumnal
allele would increase its own expression as the key is that the sum
total of expression be reduced. In this way one can see that the overall
implication is that monandrous species derived from a polyandrous state
exhibit a host of combinations of genomic imprinting as the competitive
tension between the padumnal
and madumnal alleles is released.  But, there is no positive
selection for symmetry so long as the optimal dosage level is maintained. 
The take home message is that the logical implications of Kinship Theory
maybe more circuitous than one might assume upon first examination,
and it is important to draw out the full conclusions to test the predictivity
of the theory. 

Not only does Kinship Theory
offer general predictions, it can also serve as a explanatory framework
for human pathologies.  An important example of this is Prader-Willi
Syndrome, (PWS) a malfunction of the expression of the padumnal

alleles in the chromosome 15q region.¹⁶  PWS might give
us some insights into the nature of coevolution between padumnal
and madumnal alleles, as it shows us the development of child
behavior purely under "maternal" genetic influence.  Though
the corpulence of PWS children is well known, PWS children are often
underweight at birth and do not begin to gain weight until they are
past the age of 2.  Additionally, they are known to be particularly
quiet and undemanding infants, and their eating habits in childhood
continue this trend as their "foraging" behavior shows little discernment
or discrimination as compared to the "pickiness" typical of human
young.  An evolutionary story can easily be generated for PWS in
that it shows that the optimal strategy being pursued by the madumnal

alleles is one where the offspring consumes minimal maternal resources,
at its own cost (ergo, low birth weight), does not make excessive attention
demands (ergo, quiet), and once weaning is complete is relatively single-minded
and self-sufficient in procuring and consuming a wide variety of food
stuffs without parental supervision, guidance or attention.  One
could object humans are a monandrous species, but it is important to
remember that paternity uncertainty is not unknown in our species, with
a median rate of misattributed paternity of about 3% (with wide inter-populational
variance).¹⁷  Additionally, the present day behavioral
norms of our species might not be typical of its evolutionary past. 
One crucial test of the difference in imprinting has been two species
of mice, Peromyscus manicultus
and Peromyscus polionotus.  Matings between the polyandrous
P. maniculatus and monandrous P. polionotus

seem to result offspring which exhibit the imprinting biases of the
former against the latter (maniculatus
females give birth to small offspring by polionotus males, while
polionotus females give birth to large offspring by maniculatus
males).¹⁸

The possibilities of variation
in behavior between closely related species and across evolutionary
time should be reflected in the molecular coevolution between padumnal

and madumnal alleles in an "arms race." And they do seem
to leave a molecular trace.¹⁹ One a cytosine of Igf2r
the madumnal copy is methylated in the zygote cell-stage 2, then
umethylated in stage 4, and remethylated in stage 8.  The Igf2-H19
gene complex shows evidence of 30 deletions, inserts and transgenes,
suggesting a long history of evolutionary modification.²⁰ 

Additionally, there is the added theoretical possibility of conflict
between maternal trans-acting imprinting alleles and madumnal
imprinted alleles.  The genetic reasoning is that though madumnal
imprinted alleles are related to the mother by definition (they are
inherited from the mother), imprinter alleles within the mother have
only a ½ chance of being passed with the madumnal
imprinted allele (independent transmission).  This sets up a conflict
where the trans-acting maternal allele has a stronger bias toward
increasing the fitness of the mother than the madumnal

allele.  In the language of coefficients of relatedness from the
maternal imprinter allele is r
½ to the madumnal allele, but 1 between the maternal imprinter
allele and the mother, the latter requires at least twice as much benefit
to the offspring than to the mother.  In contrast, padumnal
alleles and paternal imprinter alleles tend to exhibit less conflict
because both "agree" upon the importance of maternal investment
to increase their own fitness at minimal cost, especially in a polyandrous
species (as is the norm in mammals).²¹  Finally, an
alternative line of reasoning suggests that because of the variation
in male reproductive strategies over evolutionary time there will be
conflict between paternal and padumnal

alleles in situations where males exhibit a high degree of relatedness
to all offspring, including future ones, because of strong pair-bonds.
In contrast, the maternal and madumnal
dynamic is considered to be more stable because of the obligate nature
of female investment.  This logic implies that epigenetic imprinting
from paternal imprinting alleles will be less stable than maternal imprinting
alleles.²²  

Obviously a lot more empirical
work needs to be done to match this theoretical paper trail.  Though
the mouse has been fruitful in yielding up imprinted regions of the
genome, it is important to test the predictions of the Kinship Theory
in non-mammalian taxa which are Ovoviviparous or engage in intensive
"parental investment."  Two groups which would be good targets
are the sharks, which often give "live birth" to small broods, and
social insects, which engage in intensive rearing of their young. 
Further elucidation of within-taxa variation in imprinting needs to
be done to confirm the evolutionarily necessary covariance between polyandry
and asymmetrical expression.  The putative genetic networks that
exist must be fleshed out by a more detailed understanding of the basic
molecular mechanism of imprinting, e.g., how does an allele "know"
it is paternal or maternal in origin?  Of the 27 well characterized
regions of the mouse genome which seem subject to parental specific
imprinting, 8 of them have neurological and behavioral implications.²³ 

While in humans there have been studies which suggest a preference by
females for the smells of males who carry their padumnal
HLA profiles.²⁴  This reinforces the likelihood that
parental specific imprinting might not be common, but it is highly targeted
to loci of strong fitness import, with a neurobehavioral bias. 
Some workers hypothesize that many human mental pathologies, such as
schizophrenia, are likely to show genomic imprinting effects.²⁵ 
The possibility of medical research exploring this option is important
when human lives are at stake.  Though the molecular genetic trenches
have to be dug at some point, the theoretical-evolutionary can at least
work as scouts pointing in the general direction of new avenues of discovery
and constraining the possibilities.

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