Structural and Evolutionary Genomics

NATURAL SELECTION IN GENOME EVOLUTION Giorgio Bernardi ELSEVIER SZN

Big Bang

N. Hartmann’s “strata of existence”

(after Bernardi, 2005) Formation of the earth Origin of life Multicellular organisms

-14 -10 -5

Billions years

0 SZN

Origin of life

1. Absolutely exceptional chance event (Jacques Monod, 1970) 2. Necessary event under the prevailing physico-chemical conditions (Christian de Duve, 1995)

SZN

Jacques Monod

“Le Hasard et la Nécessité”

1970

SZN

Christian de Duve

“Vital Dust: Life as a Cosmic Imperative”

1995

Georges Cuvier

(1769 – 1832) 1. Fixity of species 2. Extinction of species

SZN

Jean-Baptiste Lamarck

“Philosophie Zoologique”

1809 • “Internal force” • Inheritance of acquired characters

SZN

Alfred R. Wallace “On the Tendency of Varieties to Depart Indefinitely from the Original Type” (1858) SZN

Charles Darwin

“The Origin of Species”

1859

SZN

Evolution: descent with modification

Charles Darwin

SZN

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

SZN

At the level of the “classical phenotype” (form and function of organisms) 1. at the trait level (natural selection ; Darwin, 1859; Wallace, 1859)

SZN

SZN

This preservation of favourable individual differences and variations [negative selection] [positive selection] or the Survival of the Fittest , and the destruction of those which are injurious variations , I have called Natural Selection, [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

SZN

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)

SZN

Ronald A. Fisher John B.S. Haldane Sewall Wright SZN

The selectionist (neo-darwinian, synthetic) theory of evolution reconciled Mendel’s laws of inheritance with evolution but neglected neutral changes

SZN

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)

SZN

The molecular clock

Time (Myr)

SZN

Biases in the replication machinery

Sueoka (1962); Freese (1962)

AT GC PROKARYOTES

25 50 75

GC SZN

Motoo Kimura

“The Neutral Theory of Molecular Evolution”

1983

SZN

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

SZN

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

SZN

The genome: an operational definition The haploid chromosome set Hans Winkler (1920)

SZN

• 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)

SZN

The prokaryotic paradigm The genome as the sum total of genes

SZN

Genome size, coding sequences and gene numbers in some representative organisms Organism

Haemophilus

Genome size a Mb b 2 Coding sequences % 85 Gene numbers a 2,000 kb/gene a, b 1 Yeast Human 12 3,200 70 2 6,000 32,000 2 100 a in approximate figures b kb, kilobases, or thousands of base pairs, bp; Mb, megabases, or millions of bp; (Gb, gigabases, are billions of base pairs)

SZN

The genome as the sum total of coding and non-coding sequences

SZN

The genome

• The bean bag view • Additive vs. cooperative properties • The integrated ensemble view

SZN

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%)

SZN

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

SZN

SZN

SZN

1 2 3 4 5 6 7 8 9 10 1 Isochore patterns Pavlicek, Paces, Clay and Bernardi 2001 Costantini, Saccone, Auletta and Bernardi 2004

Genome phenotypes

DNA Coding Sequences SZN

Compositional correlations Universal correlations

SZN

Hydrophobicity SZN

SZN

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 Chromatin structure GC Heterogeneity Gene expression Replication timing Recombination Large Closed Low Low Late Low Small Open High High Early High

Genome evolution in vertebrates

1.

Conservative mode 2.

Transitional mode

SZN

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

SZN

AT bias

Most recent common ancestor

100 Myrs

Extant mammalian orders similar isochore patterns

SZN

Genome evolution in vertebrates

The transitional mode GC increase SZN

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)

SZN

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)

SZN

3 2 Polar fish Tropical/Temperate fish 1 R = 0.50

R = 0.45

Mammals

R = 0.80

5mC, % 0 35 2 Snakes Lizards Turtles Crocodiles 40 1 0 35 45 GC, %

Mammals

40 GC, % 45 50

Polar fish

50 Varriale et al., 2005

SZN

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) SZN

Chromosomal regions in interphase nuclei

Chromatin Location GC-increase

at higher body temperature

Gene-rich

open central needed

Gene-poor

closed peripheral not needed for chromatin stability Saccone et al., 2002; Di Filippo et al., 2005

SZN

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) SZN

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)

SZN

(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; genomic fitness

SZN

Compositional optimum Structural transition 56% 55% GC 54% Negative selection Changes to AT Changes to GC Critical changes

SZN

SZN

The structural transition can be visualized as a change in DNA and chromatin structure which affects gene expression Hence negative selection

SZN

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)

SZN

Natural selection (mainly negative selection) 1. controls neutral changes at the isochore level 2. causes the shifts in the compositional transitions of the genome

SZN

T ° 51%

50%

50%

49.5 % Ratchet mechanism: Negative selection below the lower (blue) level Shift of the compositional optimum (black line)

50%

49%

SZN

SZN

CHANGES

DELETERIOUS ADVANTAGEOUS NEO-DARWINIAN VIEW NEUTRAL DARWINIAN VIEW CRITICAL NEUTRAL 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

SZN

Although the neo-selectionist theory can integrate the neutral theory, it represents a very different view of genome evolution

SZN

The dilemma of the neutral theory

(Kimura, 1983) • “Why

natural selection is so prevalent at the phenotypic level and yet random fixation of selectively clearly neutral or nearly neutral alleles

prevails at the molecular level ” ?

“laws governing molecular evolution are different from those governing

phenotypic evolution.” • “increases and decreases in the mutant

frequencies are due mainly to chance

.” “Survival of the luckiest”

SZN

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”

SZN

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.

SZN

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

SZN

SZN