Transcript Giorgio Bernardi Laboratory of Molecular Evolution Stazione Zoologica Anton Dohrn Napoli 1. Approaches to the study of evolution 2.

Giorgio Bernardi
Laboratory of Molecular Evolution
Stazione Zoologica Anton Dohrn
Napoli
1. Approaches to the study of evolution
2. The evolution of the vertebrate
genome
3. The neutralist/selectionist debate
and the neo-selectionist theory of
evolution
SZN
At the level of the “classical phenotype”
(form and function of organisms)
1. at the trait level (natural selection ; Darwin,
1858; Wallace, 1858)
SZN
I have called Natural Selection, or the
Survival of the Fittest, this preservation
of favourable individual differences and
variations and the destruction of those
which are injurious variations.
Variations neither useful nor injurious
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”
(genetic characters)
1. at the trait level (natural selection)
2. at the genetic level (selectionist theory ;
Fisher, 1930; Wright, 1931; Haldane, 1932)
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 and gene level (neutral theory;
Kimura, 1968; 1983)
SZN
The mutation-random drift theory
(the neutral theory)
(Kimura, 1983)
● “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.”
● “increases and decreases in the mutant
frequencies are due mainly to chance.”
“Survival of the luckiest”
SZN
Deleterious
Advantageous
1838-1859
Natural Selection (Darwinian) Theory
Neutral
Nearly neutral
1918-1932
Selectionist (Neo-darwinian) Theory
1969-1983
1972-2002
Neutral (Non-darwinian) Theory
Nearly Neutral Theory
SZN
The selectionist-neutralist debate
concerns
the role of chance in evolution:
is evolution a stochastic or a
deterministic process?
or both?
SZN
At the level of the “genome phenotype”
(1973; 1976)
Instead of looking at a few genes, our approach
looked at the whole genome, more specifically
at its compositional patterns,
their maintenance and their changes in evolution
SZN
Ultracentrifugation in Cs2SO4 density gradients in
the presence of sequence-specific ligands
(Ag+, BAMD; Corneo et al., 1968)
Gene (1970’s) and genome (2001, 2003) sequencing:
in silico work
SZN
THE VERTEBRATE GENOME
• Compositional compartmentalization
• Compositional correlations
• Compositional evolution
SZN
Recognition of phylogenetic differences
at the macromolecular level in the
organization of the eukaryotic genomes:
• Similarity of mammalian and avian
genomes.
• Differences between warm- and coldblooded vertebrates.
• Large-scale changes in the genome
organization have taken place during the
evolution of vertebrates.
Thiery, Macaya and Bernardi, 1976
SZN
GENOME PHENOTYPES
Xenopus
Thiery,
Macaya
and
Bernardi
1976
Human
Coding sequences, %
Xenopus
Bernardi
Human
GC3
1995
SZN
Macaya,
Thiery
and
Bernardi
1976
SZN
Costantini,
Pavlicek,
Clay,
Paces, Clay Auletta
and
and
Bernardi Bernardi
2001
2006
SZN
10
20
30
40
10
20
30
40
50 (Mb)
60
70
80
90
100 (Mb)
50
60
50
GC, %
40
30
0
60
GC, %
50
40
30
50
WINDOW: 100 kb
Costantini et al., 2006
THE HUMAN GENOME
ISOCHORE PROPERTIES
• Number:
~ 3200
• Size:
~1 Mb
• Std. Dev.:
1% GC (85%)
2% GC (15%)
SZN
ISOCHORE FAMILIES
450
L2
400
350
Size, Mb
300
L1
H1
250
200
150
H2
100
50
H3
0
33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
GC, %
Costantini et al., 2006
SZN
CHROMOSOME 21
A
(Francke, 1994;
Federico et al., 2000)
60
GC, %
B
50
850-band profile
(Costantini et al.)
40
60
GC, %
C
50
Isochore profile
(Costantini et al., 2006)
40
15
20
25
30
35
40
45 (Mb)
SZN
Compositional correlations
between coding and non-coding sequences
Bernardi et al., 1985
(updated)
SZN
Hydrophobicity
D’Onofrio et al., 2002
SZN
Amount DNA, Mb
1200
1000
800
600
400
200
0
L1
L2
H1
H2
H3
CORRELATIONS Intron, UTR size
WITH
Chromatin structure
STRUCTURE
and
FUNCTION
Gene density (genes/Mb)
ISOCHORE FAMILIES
40
30
GENE DISTRIBUTION
Genome
desert
Genome
core
20
10
0
L1
L2
H1
H2
H3
Large
Small
Closed
Open
GC heterogeneity
SINEs
LINEs
Low
Low
High
High
High
Low
Gene expression
Low
High
Replication timing
Late
Early
Recombination
Low
High
120
120
Chicken
100
100
80
80
60
60
Size, Mb
40
40
20
20
00
300
Human
250
250
200
200
150
150
100
100
50
50
00
34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 60
GC, %
SZN
800
Zebrafish
700
700
600
600
500
500
400
400
300
300
200
200
100
100
200
0
0
Medaka
150
150
100
100
Size, Mb
50
50
150
0
Stickleback
100
100
50
50
40
0
Pufferfish
30
30
20
20
10
10
00
34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58
GC, %
SZN
H. sapiens / X. laevis
H. sapiens / X. laevis
100
100
90
90
GC3 ,,%%
H. H.
sapiens
sapiens
GC
3
GC3GC
,%
H. sapiens
3, H. sapiens
H. sapiens //B.B.taurus
taurus
H. sapiens
80
70
60
50
40
30
20
y = 1.0187 x - 3.49131
R = 0.93
N = 666
10
0
80
70
60
50
40
30
20
y = 2.9761 x - 86.4378
R = 0.46
N = 1267
10
0
0
10
20
30
40
50
60
70
3 , % B. taurus
GC3GC
,%
B. taurus
80
90 100
0
10 20
30 40
50
60 70
80 90 100
X. laevis
3 , % X.
GC3GC
,%
laevis
updated by Costantini et al., 2006
SZN
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 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.
essentially stopped with the appearance of present-day
mammals and birds (an equilibrium was reached)
SZN
SZN
The formation and maintenance of
the GC-rich isochores
of warm-blooded vertebrates
is due to
NATURAL SELECTION
Selective advantages:
Increased thermodynamic stability of
DNA, RNA & proteins
The environment can mold the genome
through selection
Bernardi & Bernardi, 1986
SZN
Amino acid exchanges observed between
termophiles and the accompanying
GC-level changes in their codons
Exchange
Mesophiles
Thermophiles
Gly
Ser
Ser
Lys
Asp
Ser
Lys
→
→
→
→
→
→
→
Ala*
Ala*
Thr
Arg
Glu
Gly
Ala*
Codon
GC-level
change
0
+
0
+

+
+
Bacillaceae
GC, %
R = 0.80; ρ < 0.0001
Y = 24,393 + ,511 * X;
Musto et al., 2004
Temp
SZN
INTERPHASE NUCLEI
Location
Chromatin
GC-increase
at higher body
temperature
Gene-rich
Gene-poor
central
peripheral
open
closed
needed
not needed
for chromatin stability
Saccone et al., 2002
SZN
The conservative mode
Common ancestor of mammals
100 Myrs
AT bias
(GC→AT)
70%
base
changes
Extant mammalian orders
Conservation of
1. GC3 of orthologous genes
2. isochores
3. isochore patterns
SZN
Chr38 (14.1-18.3Mb)
14.1
45
15.1
16.1
17.1
18.1
19.1
20.1
Canis familiaris
GC, %
40
35
40
Homo sapiens
35
211
212
213
214
215
216
217
Mb
Chr1 (211-217.2Mb)
Costantini et al., 2007
SZN
“A random fixation of neutral mutants”
(i.e., the neutral theory)
cannot account for either the transitional
or for the conservative mode of evolution
YET
the majority of mutations per se can only
be neutral or nearly neutral,
because the vast majority
of the genome is non-coding,
and selection on single nucleotide
mutations is practically impossible SZN
THE CONSERVATIVE MODE OF EVOLUTION
The neo-selectionist model
DNA
GC  AT excess
changes
chromatin
SZN
THE CONSERVATIVE MODE OF EVOLUTION
The neo-selectionist model
1.
Clustering of AT-biased changes
2. trespassing a lower GC threshold (critical changes)
3. expanding changes in chromatin structure:
moving from point mutations to regional changes
4. deleterious effects on replication, transcription and,
possibly, recombination
5. negative selection of the carriers (gametes)
SZN
THE TRANSITIONAL MODE OF EVOLUTION
The neo-selectionist model
GC, %
60
50
40
Ratchet mechanism:
T°
• Shift of the lower threshold (blue broken line)
• Negative selection below the lower threshold (contribution
of positive selection)
Deleterious
1838-1859
Natural Selection (Darwinian) Theory
Advantageous
Neutral
Nearly neutral
1918-1932
Selectionist (Neo-darwinian) Theory
1969-1983
1972-2002
Critical
Neutral (Non-darwinian) Theory
Nearly Neutral Theory
1986-2006
Neo-selectionist (Ultra-darwinian) Theory
SZN
CONCLUSIONS / 1
The neo-selectionist theory provides a
solution to the neutralist/selectionist
debate: it reconciles the neutralist view
of point mutations in its more realistic
form, the nearly neutral theory of Ohta,
(now favored also by recent data on
genome transcription) with selection at
the regional level.
SZN
CONCLUSIONS / 2
The neo-selectionist theory is
an epigenomic theory,
in that compositional changes in
DNA affect chromatin
structure and physiological
chromatin remodelling.
SZN
CONCLUSIONS / 3
The neo-selectionist theory
• is an extension of Darwin’s theory
• may be seen as an ultra-darwinian theory, in
that even neutral and nearly neutral changes
are finally controlled by natural selection)
• brings us back from the
survival of the luckiest (Kimura) to the
survival of the fittest (Darwin).
SZN
Major novelties of
the neo-selectionist theory / 1
The compositional compartmentalization, the
compositional correlations between coding
and
non-coding
sequences
and
the
transitional and conservative modes of
evolution cannot be accounted for by an ATbiased point mutation process occurring at
random locations (nor by a random gene
conversion process, for that matter).
SZN
Major novelties of
the neo-selectionist theory / 2
The structural and evolutionary features
of the vertebrate genome can only be
explained by a regional process; the main
reason why the neutralist/selectionist
debate went on for so long was its focus
on the neutrality/non-neutrality of point
mutations.
SZN
Major novelties of
the neo-selectionist theory / 3
Such a regional process can only be
visualized as due to an epigenomic event
such as a change in chromatin structure,
which interferes with replication and
transcription; the coincidence between
isochores and replicon clusters explains
why the functional problems may have an
isochore dimension.
SZN
Predictions of the neo-selectionist theory
1. Genome phenotype differences in
populations
Population A
Population B
(
denote lower GC levels)
2. Genomic fitness
3. Genomic diseases
SZN
Fabio Auletta
Giuseppe Bucciarelli
Liana Cammarano
Oliver Clay
Maria Costantini
Miriam Di Filippo
Romy Sole
Giuseppe Torelli
Annalisa Varriale
Laboratorio di Evoluzione Molecolare
Stazione Zoologica Anton Dohrn
Napoli
SZN