Structural and Evolutionary
Genomics
NATURAL SELECTION
IN
GENOME EVOLUTION
Giorgio Bernardi
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ELSEVIER
N. Hartmann’s “strata of existence”
(after Bernardi, 2005)
Big Bang
-14
Formation
of the earth
-10
Billions years
Origin
of life
-5
Multicellular
organisms
0
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Origin of life
1. Absolutely exceptional chance event
(Jacques Monod, 1970)
2. Necessary event under the prevailing
physico-chemical conditions
(Christian de Duve, 1995)
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Jacques Monod
“Le Hasard et la Nécessité”
1970
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Christian de Duve
“Vital Dust: Life as a
Cosmic Imperative”
1995
Georges Cuvier
(1769 – 1832)
1. Fixity of species
2. Extinction of species
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Jean-Baptiste Lamarck
“Philosophie Zoologique”
1809
•
“Internal force”
•
Inheritance of acquired characters
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Alfred R. Wallace
“On the Tendency of Varieties to
Depart Indefinitely
from the Original Type”
(1858)
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Charles Darwin
“The Origin of Species”
1859
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Evolution:
descent with modification
Charles Darwin
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1. Classical approaches to the study of
evolution; classical theories
2. Our approach: structural and
evolutionary genomics
3. An ultra-darwinian view of evolution:
the neo-selectionist theory
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At the level of the “classical phenotype”
(form and function of organisms)
1. at the trait level (natural selection ; Darwin,
1859; Wallace, 1859)
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This preservation of favourable individual differences
and variations [positive selection], and the
destruction of those which are injurious variations
[negative selection], I have called Natural Selection,
or the Survival of the Fittest [adaptation].
Variations neither useful nor injurious
[neutral variations]
would not be affected by natural selection
and would be left either a fluctuating element, …
or would ultimately become fixed, ...
Charles Darwin
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At the level of the “classical phenotype”
(characters)
1. at the trait level (natural selection)
2. at the genetic level (selectionist theory ;
Fisher, 1930; Wright, 1931; Haldane, 1932)
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Ronald A. Fisher
John B.S. Haldane
Sewall Wright
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The selectionist
(neo-darwinian, synthetic)
theory of evolution
reconciled
Mendel’s laws of inheritance
with evolution
but neglected neutral changes
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At the level of the “classical phenotype”
(proteins and expression)
1. at the trait level (natural selection)
2. at the genetic level (selectionist theory)
3. at the protein level (Zuckerkandl and Pauling, 1962;
Sueoka, 1962; Freese, 1962; Kimura, 1968; 1983)
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Amino acid differences
The molecular clock
Time (Myr)
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Biases in the replication machinery
Sueoka (1962); Freese (1962)
AT
GC
PROKARYOTES
25
50
75
GC
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Motoo Kimura
“The Neutral Theory of
Molecular Evolution”
1983
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The mutation-random drift theory
(the neutral theory)
“the main cause of evolutionary change at
the molecular level - changes in the genetic
material itself - is random fixation of
selectively
neutral
or
nearly
neutral
mutants ”.
(Kimura, 1983)
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At the level of the “genome phenotype”
(Bernardi et al., 1973, 1976)
Instead of looking at a few genes, this approach
looked at the whole genome, more specifically
at its compositional patterns and their evolution,
moving, therefore, from the genetic level
to the genomic level
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The genome: an operational definition
The haploid chromosome set
Hans Winkler (1920)
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• constant amount of DNA per cell in any
given organism (Boivin et al., 1948;
Mirsky and Ris, 1949)
• c-value, or constant value (Swift, 1950)
• genome size (Hinegardner, 1976)
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The prokaryotic paradigm
The genome as
the sum total of genes
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Genome size, coding sequences and gene
numbers in some representative organisms
Organism
Genome size a
Coding
sequences
Gene
numbers a
2
%
85
2,000
1
12
70
6,000
2
3,200
2
32,000
100
Mb b
Haemophilus
Yeast
Human
a
b
kb/gene a, b
in approximate figures
kb, kilobases, or thousands of base pairs, bp; Mb, megabases, or
millions of bp; (Gb, gigabases, are billions of base pairs)
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The genome as
the sum total of coding
and
non-coding sequences
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The genome
• The bean bag view
• Additive vs. cooperative properties
• The integrated ensemble view
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Vertebrates
1. are a very small phylum
2. have common genetic background
(vertebrates share most genes)
3. have a large genome (~ 3000 Mb; with
coding sequences representing < 3%)
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Structural genomics of vertebrates:
our main conclusions
(i)
Genome compartmentalization (1973, 1976)
(discontinuous compositional heterogeneity, isochores)
(ii) Genome phenotype (1976, 1986)
(compositional patterns of isochores and coding
sequences)
(iii) Genomic code
compositional correlations
● between coding sequences and
- non-coding sequences (1984)
- thermal stability of proteins (1986)
● among codon positions (universal correlation; 1992)
● First evidence that the eukaryotic genome is an
integrated ensemble: no junk DNA)
● Incompatibility with neutral theory
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Isochore patterns
1
2
1
3
4
5
6
7
8
9
10
Costantini,
Pavlicek,
Saccone,
Paces, Clay
Auletta
and
and
Bernardi
Bernardi
2001
2004
Genome phenotypes
DNA
Coding Sequences
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Compositional correlations
Universal correlations
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Hydrophobicity
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Gene distribution
• Bernardi et al., 1984
• Mouchiroud et al., 1991
• Zoubak et al., 1996
• Lander et al., 2001
Correlations with structure and function
Intron, UTR size
Large
Small
Chromatin structure
Closed
Open
GC Heterogeneity
Low
High
Gene expression
Low
High
Replication timing
Late
Early
Recombination
Low
High
Genome evolution
in vertebrates
1.
Conservative mode
2.
Transitional mode
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Genome evolution in vertebrates
The conservative mode
Mammalian orders are characterized
by
•
a star-like phylogeny (over 100 Myrs)
•
a strong mutational AT bias
(GC  AT; mC  T)
•
a conservation of base composition,
methylation and CpG levels
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Most recent
common ancestor
AT bias
Extant
mammalian orders
similar isochore patterns
100 Myrs
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Genome evolution in vertebrates
The transitional mode
GC increase
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THE COMPOSITIONAL TRANSITIONS:
(cold- to warm-blooded vertebrates)
Compositional changes
1.
concerned the (gene-dense) ancestral genome core
2.
affected both coding and non-coding sequences (at
comparable and correlated levels)
3.
occurred (and were similar) in the independent ancestral
lines of mammals and birds (convergent evolution)
4.
did not affect cold-blooded vertebrates (with exceptions)
5.
stopped with the appearance of present-day mammals and
birds (an equilibrium was reached)
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The formation and maintenance of
GC-rich isochores
is due to
NATURAL SELECTION
Selective advantages:
Increased thermodynamic stability of
DNA, RNA & proteins
(Bernardi and Bernardi, 1986)
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5mC, %
3
Polar fish
Tropical/Temperate
fish
2
R = 0.50
R = 0.45
R = 0.80
1
Mammals
5mC, %
0
35
40
Snakes
45
GC, %
Lizards
50
Varriale
et al., 2005
Polar fish
Turtles
2
Crocodiles
1
Mammals
0
35
40
45
GC, %
50
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The compositional transitions
affected
1. only a small part of the genome
(the ancestral genome core)
2. both coding and non coding sequences
(at comparable and correlated levels)
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Chromosomal regions in interphase nuclei
Chromatin
Location
GC-increase
at higher body
temperature
Gene-rich
Gene-poor
open
closed
central
peripheral
needed
not needed
for chromatin stability
Saccone et al., 2002; Di Filippo et al., 2005
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The genome compartmentalization,
the genome phenotype and
the genomic code,
the conservative and transitional modes
of genome evolution
cannot be accounted for by
“a random fixation of neutral mutants”
(i.e., by the neutral theory)
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YET
the majority of mutations per se
can only be neutral or nearly
neutral (if for no other reason
that the vast majority of the
genome is non coding)
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(Bernardi, 2004)
1. explains how
natural selection can take place at the
isochore level
2. reconciles
the neutral theory with natural selection
3. makes predictions:
genome phenotype differences in populations;
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genomic fitness
56%
Compositional
optimum
55%
GC
54%
Negative
selection
Structural
transition
Changes to AT
Changes to GC
Critical changes
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The structural transition
can be visualized as
a change in DNA and chromatin structure
which affects
gene expression
Hence
negative selection
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Isopycnic
expression of
integrated viral
sequences
•
BLV
(Kettmann et al., 1979)
•
HBV
(Zerial et al., 1986)
•
MMTV (Salinas et al., 1987)
•
RSV
•
HTLV-1 (Zoubak et al., 1994)
•
HIV-1
(Rynditch et al., 1991; 1998)
(Tsyba et al., 1992; 2004)
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Natural selection
(mainly negative selection)
1. controls neutral changes at the
isochore level
2. causes the shifts in the compositional
transitions of the genome
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51%
50%
50%
49.5 %
T°
50%
49%
Ratchet mechanism:
Negative selection below the lower (blue) level
Shift of the compositional optimum (black line)
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CHANGES
NEUTRAL
DARWINIAN VIEW
CRITICAL
DELETERIOUS
NEUTRAL
ADVANTAGEOUS
NEO-DARWINIAN
VIEW
NEUTRAL VIEW
ULTRA-DARWINIAN
VIEW
Predictions of the neo-selectionist theory
1. Genome phenotype differences in
populations
Population A
Population B
(
denote lower GC levels)
2. Genomic fitness
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Although
the neo-selectionist theory
can integrate
the neutral theory,
it represents a very different view
of genome evolution
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The dilemma of the neutral theory
(Kimura, 1983)
• “Why natural selection is so prevalent at the
phenotypic level and yet random fixation of
selectively neutral or nearly neutral alleles
prevails at the molecular level ” ?
“laws governing molecular evolution are
clearly different from those governing
phenotypic evolution.”
• “increases and decreases in the mutant
frequencies are due mainly to chance.”
“Survival of the luckiest”
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According to the neo-selectionist theory
natural selection operates
not only on
1. the classical phenotype
(form and function; proteins and expression)
but also on
2. the genome phenotype
(compositional patterns and functional
implications)
“Survival of the fittest”
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1.
The eukaryotic genome is an integrated ensemble of
compositionally
correlated
coding
and
non-coding
sequences: there is no junk DNA.
2.
Isochore patterns (genome phenotypes) are stable or
changing depending upon environmental conditions.
3.
The GC increases accompanying the transition from coldto warm-blooded vertebrates are advantageous because
they stabilize thermodynamically DNA, RNA and proteins.
4.
Changes only affect the (gene-dense) genome core because
of its open chromatin structure.
5.
The neo-selectionist theory (an ultra-darwinian theory)
explains how natural selection controls neutral changes at
the isochore level and causes shifts in compositional
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genome transitions.
Acknowledgements
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Fernando Alvarez, Montevideo
Stilianos Arhondakis, Naples
Fabio Auletta, Naples
Oliver Clay, Naples
Stéphane Cruveiller, Naples/Paris
Maria Costantini, Naples
Giuseppe D’Onofrio, Naples
Kamel Jabbari, Paris
Héctor Musto, Montevideo
Adam Pavlicek, Prague/Paris
Edda Rayko, Paris
Alla Rynditch, Kiev
Salvo Saccone, Catania
Giuseppe Torelli, Naples
Annalisa Varriale, Naples
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