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STRUCTURAL AND FUNCTIONAL DIVERSITY
OF THE EUKARYOTIC GENOME
Brno, Czech Republic, October 14-16, 2010
Metaptation:
Metaphors for Genome Evolution
David G. King
Southern Illinois University Carbondale
U.S.A.
Metaphor
an implicit comparison; a tool for thinking.
Metaptation
a neologism; the subject of this talk.
a fable of a
grasshopper . . .
Image by Milo Winter
Aesop’s Fables, 1919
Image by Milo Winter
Aesop’s Fables, 1919
Genes need
“tuning knobs” !
Simple Sequence Repeats
behave like tuning knobs.
Incremental adjustability
Repeat number mutations typically exert
small effects on phenotype.
Reversibility
Any shift in repeat number can be readily
reversed.
Modularity
Each example has its own characteristics.
A tuning knob has dual functionality.
A concrete function:
a “setting” (parameter value).
An abstract function:
a “protocol” (adjustability).
Protocol of adjustability
Protocol of adjustability
embodied by simple sequence repeats
Motifs
Functional domains
Microsatellites
practically anywhere!
mononucleotides
exons
e.g., polyA • polyT
dinucleotides
e.g., ACn • GTn
trinucleotides
e.g., CAGn • CTGn
introns
UTRs
upstream, downstream
tetra-, penta-, hexanucleotides
Minisatellites
longer motifs, up to tens of nucleotides
et cetera
A protocol is an implicit rule or architecture
that defines permissible avenues for behavior.
A genetic protocol imposes "grammatical"
constraints on genetic variation.
An advantageous genetic protocol
enhances the probability of beneficial
mutation.
Some advantageous protocols.
(adaptively plausible constraints on genetic variation)
Incremental adjustability (simple sequence repeats).
Cut and paste (transposable elements).
Mix and match (meiotic recombination).
Programmed gene rearrangement (e.g., trypanosomes).
On / off switching (bacterial contingency genes).
Many more . . . ?
Questions of protocol
Do evolutionary protocols just happen (by accident)?
or
Have protocols evolved because they are evolutionarily
advantageous?
If protocols have evolved, how could this be
possible?
A conceptual difficulty . . .
An advantageous protocol can raise the
mutation rate for variation arising within the
constraints of the protocol.
But the idea that mutation rates might increase
for evolutionary advantage is contrary to
conventional evolutionary theory.
Image from Wikipedia Commons
Natural selection of mutation rates has only one possible
direction, that of reducing the frequency of mutation
to zero.
Evolution has probably reduced mutation rates to far below
species optima, as the result of unrelenting selection for
zero mutation rate in every population.
George C. Williams
Adaptation and Natural Selection, 1966
If genetic variation arises within the
constraints of a protocol, selection
for those variants must indirectly
select the protocol.
Image from Wikipedia Commons
A semantic difficulty . . .
Protocols cannot be adaptations,
because an “adaptation” by definition
is shaped by natural selection.
And protocols are invisible
to natural selection.
Image from Wikipedia Commons
Natural selection shapes adaptations
by acting on phenotypes.
Natural selection sees the grasshopper.
Natural selection cannot see the
the implicit protocols in the
grasshopper’s genome.
Image from Wikipedia Commons
A simple semantic solution:
If an advantageous protocol cannot
properly be called an adaptation,
Let us call it a “metaptation.”
Image from Wikipedia Commons
An adaptation is an advantageous
phenotypic trait.
The process of adaptation is how such
phenotypic traits evolve, by natural
selection for fitness.
***
A metaptation is an advantageous
genetic protocol.
The process of metaptation is how
protocols evolve by indirect
selection.
Image from Wikipedia Commons
Metaptation
[meta, change, transcend + aptation, fitness]
1. an evolutionary process by which natural selection
indirectly shapes genomic “protocols” that
facilitate evolutionary adaptation.
2. any of the resulting “protocols for
effective evolution”.
Evolutionary Theory (1985) 7:22
Image from Wikipedia Commons
A metaptation is a genomic pattern or
architecture – a protocol – which constrains
the effect of mutation and enhances
the probability of adaptive benefit.
Image from Wikipedia Commons
What the devil determines each particular
variation? What makes a tuft of feathers come
on a cocks head, or moss on a moss rose?
Charles Darwin
letter to T.H. Huxley, 25 Nov 1859
A grand and almost untrodden field of
inquiry will be opened, on the causes and
laws of variation . . .
Charles Darwin
On the Origin of Species, 1859
Available at
www.zoology.siu.edu/king/Brno.htm
reference list
text of talk
PowerPoint slides
Image by Milo Winter
Aesop’s Fables, 1919
Simple sequence repeats / Indirect selection for "tuning knobs"
Evolutionary protocols (other than “tuning knobs”)
King DG (1985) Metaptation: A descriptive category for evolutionarily versatile
patterns of genetic and ontogenetic organization. Evol Theor 7: 222.
Arber W (2005) Gene products with evolutionary functions. Proteomics 5: 2280-2284.
Trifonov EN (1989) The multiple codes of nucleotide sequences. Bull Math Biol 51:
417–432.
Gerber H-P et al. (1994) Transcriptional activation modulated by homopolymeric
glutamine and proline stretches. Science 263: 808-811.
Barry JD (2006) Implicit information in eukaryotic pathogens as the basis of antigenic variation.
In: Caporale LH, ed. The Implicit Genome. Oxford: Oxford University Press, pp. 91-106.
Bayliss CD, Moxon ER (2006) Repeats and variation in pathogen selection. In: Caporale LH,
ed., The Implicit Genome. Oxford: Oxford University Press, pp. 54-76.
Caporale LH (1999) Chance favors the prepared genome. In: Caporale, L. H., ed. Molecular
Strategies in Biological Evolution, Ann. N. Y. Acad. Sci. 870: 1-21.
Rosenberg SM et al. (1994) Adaptive mutation by deletions in small mononucleotide
repeats. Science 265: 405-407.
Caporale LH (2000) Mutation is modulated: Implications for Evolution. Bioessays 22: 388-395.
Kashi Y, King DG, and Soller M (1997) Simple sequence repeats as a source of
quantitative genetic variation. Trends in Genetics 13: 74-78.
Caporale LH. (2003) Natural selection and the emergence of a mutation phenotype: An update
of the evolutionary synthesis considering mechanisms that affect genomic variation. Ann. Rev.
Microbiol. 57: 465-485.
King DG, Soller M, and Kashi Y (1997) Evolutionary tuning knobs. Endeavour 21:
36-40.
King, DG, and Soller, M (1999) Variation and fidelity: The evolution of simple
sequence repeats as functional elements in adjustable genes. In: S.P. Wasser, ed.,
Evolutionary Theory and Processes: Modern Perspectives, Kluwer Academic
Publishers, Dordrecht, pp. 65-82.
Fondon III JW and Garner, HR (2004) Molecular origins of rapid and continuous
morphological evolution. PNAS 101(52): 18058-18063.
Li Y-C et al. (2004) Microsatellites within genes: Structure, function, and evolution.
Mol Biol Evol 21: 991-1007.
Verstrepen KJ et al. (2005) Intragenic tandem repeats generate functional variability.
Nature Genet 37: 986–990.
Kashi Y and King DG (2006a) Simple sequence repeats as advantageous mutators in
evolution. Trends Genet 22: 253-259.
Kashi Y and King DG (2006b) Has simple sequence repeat mutability been selected
to facilitate evolution? Isr J Ecol Evol 52: 331-342.
King DG, Trifonov EN, and Kashi, Y (2006) Tuning knobs in the genome: Evolution
of simple sequence repeats by indirect selection. In: LH Caporale, ed., The Implicit
Genome, Oxford University Press, pp. 77-90.
King DG and Kashi Y (2007a) Mutability and Evolvability: Indirect selection for
mutability. Heredity 99: 123-124.
King DG and Kashi Y (2007b) Mutation rate variation in eukaryotes: evolutionary
implications of site-specific mechanisms. Nature Rev Genet 8 (doi:10.1038/nrg2158c1).
Vinces MD, Legendre M, Caldara M et al. (2009) Unstable tandem repeats in
promoters confer transcriptional evolvability. Science 324: 1213-1216.
Caporale LH (2003) Foresight in genome evolution. Amer. Sci.. 91: 234-241.
Caporale LH (2006) The Implicit Genome. Oxford: Oxford University Press, pp. 91-106.
Csete M and Doyle J (2002) Reverse engineering of biological complexity. Science 295: 16641669.
Doyle J, Csete M and Caporale LH (2006) An engineering perspective: The implicit protocols.
In: Caporale LH, ed., The Implicit Genome. Oxford: Oxford University Press, pp. 294-298.
Doyle & Csete (2007) Rules of engagement. Nature 446: 860.
Kirschner M and Gerhart J (1998) Evolvability. Proc. Natl. Acad. Sci. USA 95: 8420-8427.
Mihola O et al. (2009) A Mouse Speciation Gene Encodes a Meiotic Histone H3
Methyltransferase. Science 328:373-375.
Oliver KR, Green WK (2009) Transposable elements: powerful facilitators of evolution.
BioEssays 31: 703–714.
Shapiro JA (1983) Variation as a genetic engineering process. Pp. 253-270, in D.S. Bendall, ed.
Evolution from Molecules to Men, Cambridge University Press, Cambridge.
Shapiro JA (1997) Genome organization, natural genetic engineering and adaptive mutation.
Trends Genet 13:98-104.
Thaler D (1994) The evolution of genetic intelligence. Science 264: 224-225.
Contrary literature
Bridges CB (1919) Specific modifiers of eosin eye color in Drosophila melanogaster. J Exp
Zool 28(3): 37-384.
Sturtevant AH (1937) Essays on evolution. I. On the effects of selection on mutation rate. Q Rev
Biol 12: 464-467.
Williams GC (1966) Adaptation and Natural Selection. Princeton: Princeton University Press,
1966.
Sniegowski PD, Gerrish PJ, Johnson T et al. (2000) The evolution of mutation rates: separating
causes from consequences. Bioessays 22: 1057-1066.
Sniegowski PD, Murphy HA (2006) Evolvability. Current Biology 16: R831-R834.
In everyday usage, protocols are rules designed to manage relationships and
processes smoothly and effectively.
If modules are ingredients, parts, components, subsystems, and players, then
protocols describe the corresponding recipes, architectures, rules, interfaces,
etiquettes, and codes of conduct.
Protocols here are rules that prescribe allowed interfaces between modules,
permitting system functions that could not be achieved by isolated modules.
Protocols also facilitate the addition of new protocols and organization into
collections of mutually supportive protocol suites.
Thinking in terms of protocols, in addition to genes, organisms, and
populations, as foci of natural selection, may be a useful abstraction for
understanding the evolution of complexity.
Good protocols allow new functions to be built from existing components
and allow new components to be added or to evolve from existing ones,
powerfully enhancing both engineering and evolutionary “tinkering.”
Successful protocols become highly conserved because they
both facilitate evolution and are difficult to change.
Marie Csete and John Doyle 2002 (Science 295:1664)
Far from being clumsy stumblers into random point
mutations, genomes have evolved mechanisms that
facilitate their own evolution.
These mechanisms diversify a genome and increase
the probability that its descendants will survive.
Lynn Helena Caporale 1998 (Annals N.Y. Acad. Sci. 870)
Any organism as it now exists must be regarded as a very
complex physicochemical machine with delicate adjustments
of part to part. Any haphazard change made in this mechanism
would almost certainly result in a decrease of efficiency.
Only an extremely small proportion of mutations may be
expected to improve a part or the interrelation of parts in such
a way that the fitness of the whole organism for its available
environments is increased.
Bridges 1919 (J Exp Zool 28 [3]: 37)
It seems at first glance that there should be a counter-selection, due to the occurrence of
favorable mutations. It is true that favorable mutations furnish the only basis for
improvement of the race, and must be credited with being the only raw material for
evolution. It would evidently be fatal for a species, in the long run, if its mutation rate
fell to zero, for adjustment to changing conditions would then not long remain possible.
While this effect may occur, it is difficult to imagine its operation. . .
[F]or every favorable mutation, the preservation of which will tend to increase the
number of genes in the population that raises the mutation rate, there are hundreds of
unfavorable mutations that will tend to lower it. Further, the unfavorable mutations are
mostly highly unfavorable, and will be more effective in influencing the rate than will
the relatively slight improvements that can be attributed to the rare favorable mutations.
[W]hy does the mutation rate not become reduced to zero? No answer
seems possible at present, other than the surmise that the nature
of genes does not permit such a reduction. In short,
mutations are accidents, and accidents will happen.
Sturtevant 1937 (Q Rev Biol 12: 464)
One frequently hears that natural selection will not produce too low a
mutation rate because that would reduce the evolutionary plasticity of the
species.
[N]atural selection of mutation rates has only one possible direction, that
of reducing the frequency of mutation to zero. That mutations should
continue to occur requires no special explanation. It is merely a reflection
of the unquestionable principle that natural selection can often produce
mechanisms of extreme precision, but never of perfection. . .
Evolution has probably reduced mutation rates to far below species
optima, as the result of unrelenting selection for zero mutation rate in
every population.
George Williams
Adaptation and Natural Selection, 1966
[I]t can be appealing to suppose that the genomic mutation rate is adjusted to a
level that best promotes adaptation. Most mutations with phenotypic effects are
harmful, however, and thus there is relentless selection within populations for
lower genomic mutation rates. Selection on beneficial mutations can counter
this effect by favoring alleles that raise the mutation rate, but the effect of
beneficial mutations on the genomic mutation rate is extremely sensitive to
recombination and is unlikely to be important in sexual populations.
The physiological cost of reducing mutation below the low level observed in
most populations may be the most important factor in setting the genomic
mutation rate in sexual and asexual systems, regardless of the benefits of
mutation in producing new adaptive variation. Maintenance of
mutation rates higher than the minimum set by this 'cost of fidelity'
is likely only under special circumstances.
Sniegowski et al. 2000 (BioEssays 22:1057)
Some authors believe it to be as much the function of
the reproductive system to produce individual
differences, or very slight deviations of structure, as to
make the child like its parents.
Charles Darwin
On the Origin of Species, 1859
Drosophila melanogaster
cervical connective
Psychodidae
Rhagionidae
Asilidae
Empididae
Dolichopodidae
Muscidae
Anthomyiidae
Micropezidae
Glossinidae
Charles Darwin again:
A grand and almost untrodden field of inquiry will be opened,
on the causes and laws of variation . . .
Can we find protocols for mutation, which can facilitate the
evolutionary adjustment of adaptive traits, such as details of
individual nerve cells?
Ephydridae
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