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Structural and Evolutionary
GenomicsNATURAL SELECTION
IN GENOME EVOLUTION
Giorgio Bernardi
ELSEVIER
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N. Hartmann’s “strata of existence” (after Bernardi, 2005)
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Billions years
Big Bang Formation of the earth
Origin of life
Multicellular organisms
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Origin of lifeOrigin 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 MonodJacques Monod
“Le Hasard et la Nécessité”
1970
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Christian de DuveChristian de Duve
“Vital Dust: Life as a Cosmic Imperative”
1995
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Georges CuvierGeorges 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. WallaceAlfred R. Wallace
“On the Tendency of Varieties to
Depart Indefinitelyfrom the Original Type”
(1858)
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Charles DarwinCharles 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 classical
phenotypephenotype”
(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 SelectionNatural Selection, or the Survival of the Fittest
[adaptation].Variations neither useful nor injurious
[neutral variations]would not be affected by natural selectionwould 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 classical
phenotypephenotype”
(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 phenotypeclassical 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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The molecular clockThe molecular clock
Time (Myr)
Am
ino a
cid
diff
ere
nce
s
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PROKARYOTES
25 50 75
GC
AT GC
Biases in the replication Biases in the replication machinerymachinery
Sueoka (1962); Freese (1962)
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Motoo KimuraMotoo 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)SZN
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At the level of the “genome phenotypegenome 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 levelSZN
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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 paradigmThe 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
Mb b
Coding sequence
s %
Gene numbers a
kb/gene a, b
Haemophilus
2 85 2,000 1
Yeast 12 70 6,000 2
Human 3,200 2 32,000 100
a in approximate figuresb 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)
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● First evidence that the eukaryotic genome is an integrated ensemble: no junk DNA)● Incompatibility with neutral theory
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1
2
3
4
5
1
6
7
8
9
10
Isochore patterns
2004
Costantini,Saccone,Auletta
and Bernardi
2001
Pavlicek, Paces, Clay
and Bernardi
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Genome phenotypes
DNA Coding Sequences
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Universal correlations
Compositional correlations
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Hydrophobicity
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Intron, UTR size Large Small
Chromatin structure Closed Open
GC Heterogeneity Low High
Gene expression Low High
Replication timing Late Early
Recombination Low High
Gene distribution
Correlations with structure and function
•Bernardi et al., 1984
•Mouchiroud et al., 1991
•Zoubak et al., 1996
• Lander et al., 2001
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Genome evolutionGenome evolutionin vertebratesin vertebrates
1. Conservative mode
2. Transitional mode
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Genome evolution in Genome evolution in vertebratesvertebrates
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 SZN
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Most recentcommon ancestor
Extant mammalian orders
similar isochore patterns
100 MyrsAT bias
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Genome evolution in Genome evolution in vertebratesvertebrates
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 SELECTIONSelective advantages:
Increased thermodynamic stability of
DNA, RNA & proteins
(Bernardi and Bernardi, 1986)
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Varrialeet al., 2005
1
2
3Polar fish
Tropical/Temperate fish
R = 0.50
R = 0.45
Mammals
R = 0.80
5m
C,
%
0
GC, %
35 40 45 505mC, %
0
1
2
35 40 45 50
GC, %
Snakes
Lizards
Turtles
Crocodiles
Mammals
Polar fish
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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
Gene-rich Gene-poor
Chromatin open closed
Location central peripheral
GC-increase at higher body temperature
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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YETthe 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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1. explains hownatural selection can take place at the isochore level
2. reconcilesthe neutral theory with natural selection
3. makes predictions:genome phenotype differences in populations; genomic fitness
(Bernardi, 2004)
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Negative selection
Structural transition
Compositional optimum
56%
55%
54%
GC
Changes to AT Changes to GC Critical
changesSZN
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The structural transition
can be visualized as
a change in DNA and chromatin
structure
which affects
gene expression
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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 (Rynditch et al., 1991; 1998)
•HTLV-1 (Zoubak et al., 1994)
•HIV-1 (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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Negative selection below the lower (blue) level
Shift of the compositional optimum (black line)
50%
49%
51%
50%
50%49.5 %
T°
Ratchet mechanism:
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CHANGECHANGESS
NEUTRAL
DARWINIAN VIEWDARWINIAN VIEW
ADVANTAGEOUS
DELETERIOUS
NEO-DARWINIAN NEO-DARWINIAN
VIEWVIEWULTRA-DARWINIAN ULTRA-DARWINIAN
VIEWVIEW
NEUTRAL
NEUTRAL VIEWNEUTRAL VIEW
CRITICAL GENETIC
SGENOM
ICS
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Predictions of the neo-selectionist theory
1. Genome phenotype differences in populations
( denote lower GC levels)
2. Genomic fitness SZN
Population A
Population B
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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” SZN
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1. the classical phenotype (form and function; proteins and
expression)
SZN“Survival of the fittest”
According to the neo-selectionist theory natural selection operates
not only on
2. the genome phenotype (compositional patterns and functional implications)
but also on
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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 cold- to 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 genome transitions.
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Acknowledgements• 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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