Download Diapositiva 1 - Curso de Sistemática IB 2010

Ejercicios de alineamiento de secuencias: CLUSTALW insertar secuencias de FASTA
Pedir alineamiento múltiple
Analizar resultado
Regiones conservadas y variables en proteinas
Codones y aminoácidos
The 20 amino acids have overlapping properties
Small change
big change
Relationship between physico-chemical difference and relative
substitution frequency
Minor changes are
more frequent
Drastic changes
are infrequent
Kimura (1983) The neutral theory of molecular evolution.
Pseudogenes as a paradigm of neutral evolution
Pseudogenes show an extremely high rate of nucleotide substitution.
Li, Gojobori and Nei (1981) Nature 292: 237-239
Conservation in a ‘typical’ gene
Splice sites
Start of translation
Start of transcription
Polyadenylation site
On the basis of 3,165 human-mouse pairs
MGSC Nature (2002) 420 520-562
Degeneracy of the Genetic Code
nonsynonymous
synonymous
Each of the 61 sense codons can mutate in 9 different ways
of the 549 possible changes are synonymous
Colors represent
amino acids
134
Synonymous changes can be neutral mutations
•
If most DNA changes were due to adaptive evolution than one
would imagine that most changes would occur in the first and
second codon positions.
•
If DNA divergence includes neutral mutations, then the third
position should change more rapidly because synonymous
mutations are more likely to be neutral.
King, J. L., and Jukes, T. H. 1969. Non-Darwinian evolution, Science 164, 788-798.
Preponderance of changes in the 3rd position
The first 220 nucleotides of human and mouse renin binding protein
The third position of all codons are marked
Of the 31 changes:
4 - 1st position
4 - 2nd position
23 - 3rd position
Estimating separately the rate of synonymous change and
non-synonymous change
•
KS = number of Synonymous substitutions per synonymous site
•
KA = number of non-synonymous (Altering) substitutions per
non-synonymous site
One way of estimating Ks and Ka would be to examine each change
individually and check if it is synonymous or not. In the following we
present a method for doing this in a systematic manner.
Nucleotide sites can be classified into 3 types of degenerate sites
2-fold
Degenerate
changes of this
nucleotide relate
to pairs of
codons for the
same AA
4-fold
degenerate –
changes of this
nucleotide
relate to 4
codons for the
same AA
Synonymous
(AA = amino acids)
- Altering
0-fold
degenerate no change at
this nucleotide
leaves coding
for the same
AA
4-fold degenerate sites are found in 32 of the 3rd
position of 61 codon sites
2-fold degenerate sites are found in 25 of the 3rd positions
and 8 of the 1st position
0-fold degenerate sites are found in 2nd position sites of
all codons (61) and in of 53 of the 1st position sites
Classify each site in a sequence according to the degeneracy of the sites.
002
002 004
004
002 002 004
004
002
002 004
004
002 002 004
004
202
002
002
002 204
004
204
004
202
002
000
002 204
004
204
004
002
002
004
004 - - -
002
004
004
002
002
004
004 - - -
002
004
004
004
004 004
004 - - -
002
202
002
004
004 004
004 000
002
202
002
Classify each site in a sequence according to the degeneracy of the sites.
000002002002204002004204002004000002002004004004002002204002004004004
000002002002204002004204002004000002002004004002002002204002004004002
Counting the number of 4-,2-,0-fold sites
(taking the average between the two sequences)
L0= (45+45)/2 = 45
L2= (13+15)/2 = 14
L4= (10+8)/2 = 9
Classify the differences with another sequence as
a. transition (S) or transversion (V)
b. degeneracy (0,2,4)
0-fold
2-fold
4-fold
transition
S0
S2
S4
transversion
V0
V2
V4
The key simplification is the special relationship between
transition/transversion and degeneracy:
Synonymous mutations
0-fold
2-fold
4-fold
transition
S0
S2
S4
transversion
V0
V2
V4
Non-synonymous mutations
(Exceptions: 1st position of arginine (CGA,CGG,AGA,AGG),
last position of isoleucine (AUU, AUC, AUA)).
We distinguish between transitions and transversions according to the
Kimura model
A




C
G

  = transitions
 = transversions
T
Use Kimura’s 2-parameter model to estimate
the numbers of transitions (Ai) and transversions (Bi) per i-th type site.
Calculate the proportions of transitional and transversional differences:
Pi = Si/Li
(12/70)
Qi = Vi/Li
(3/70)
Kimura model is used to correct for multiple hits:
The Kimura model is similar to the Jukes-Cantor
model (from the previous lecture) but also takes
into consideration that transitions and transversions
occur at different frequencies
Ai = (1/2) ln (1/(1- 2Pi – Qi)) – (1/4) ln (1/(1- 2Qi))
Bi = (1/2) ln (1/(1- 2Qi))
(~6 times more
transitions than
transversions)
(0.242)
(0.045)
The Molecular Clock of Viral Evolution
Different rates
Relationship between the number of nucleotide substitutions and the difference in the
year of isolation for the H3 hemagglutinin gene of human influenza A viruses. All
sequence comparisons were made with the strain isolated in 1968.
Gojobori et al. 1990 PNAS 87 10015-10018