structural and evolutionary genomics natural selection in genome evolution giorgio bernardi

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

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

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

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

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

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

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

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

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

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

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)

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)

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

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

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

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.

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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