Transcript Diapositiva 1 - Universidad Autonoma de Madrid

Some basics:
Homology = refers to a structure, behavior, or
other character of two taxa that is derived
from the same or equivalent feature of a
common ancestor.
• Homology applies to nucleotide sequences:
gtcccat
gtctcat
A substitution has occurred at position 4.
Sequence alignment:
•
Rapid sequence divergence or divergence over many generations
can leave little in common between two sequences and make
alignment difficult or impossible.
•
Indels ~ may be impossible to distinguish between an insertion in
one sequence and a deletion in another sequence.
example: mtDNA 12S rRNA in six genera of “stifftail” ducks
CCACCT-GT---TTCAAAA-CTCAGGCCTT
TCACCTAGC---TCCAAA--C-TAGGCCTT
CTGCCT-AC---TTCCC---C-CAGGCCTT
TCGCCT-AC---T-CAA---C-CAGGCTTT
TCGCCT-ACATTTTCCC---C-CAGGCTTT
•
Many alignment methods exist; all use algorithms that
seek to maximize the number of possible matching
nucleotides or amino acids and minimize the number
of indels.
Maximum Parsimony
Occam’s Razor
Entia non sunt multiplicanda praeter
necessitatem.
William of Occam (1300-1349)
The best tree is the one which requires the least number of
substitutions
Most parsimonious
taxon 1
taxon 2
outgroup
taxon 1
outgroup
Less parsimonious
taxon 2
Assumptions: independence
• Assumes that change at one
site has no effect on other
sites
• Good example is in RNA
stem-loop structures
• Substitution may result in
mismatched bases and
decreased stem stability
• Compensatory change may
occur to restore WatsonCrick base pairing
A
G
A
C C C CU U
GGGG A A
G
C
A
U
G
C C C C U U
C
A
GGG C A A
G
U
A
G
C C CGU U
GGG C A A
G
C
A
U
Types of substitution
A
G
C
T
• Substitutions that exchange
a purine for another purine
or a pyrimidine for another
pyrimidine are called
transitions
• Substitutions that
exchange a purine for a
pyrimidine or vice-versa
are called transversions
Differing rates of DNA evolution
• Functional constraints (particular features of coding regions,
particular features in 5' or 3’ untranslated regions)
• Variation among different gene regions with different
functions (different parts of a protein may evolve at different
rates).
• Within proteins, variations are observed between
– surface and interior amino acids in proteins (order of
magnitude difference in rates in haemoglobins)
– charged and non-charged amino acids
– protein domains with different functions
– regions which are strongly constrained to preserve
particular functions and regions which are not
– different types of proteins -- those with constrained
interaction surfaces and those without
Assumptions: variation in substitution rate
across sites
4
3.5
Substitution / site / 109 years
3
2.5
2
1.5
1
0.5
0
• All sites are not equally
likely to undergo a
substitution
Paleocene
Jurassic
Triassic
Permian
Carboniferous
Devonian
Silurian
140
100
200
300
400
500
600
700
Huronian
Carp/Lamprey
i
V ertebrates/
Insects
Reptiles/Fish
h
Algonkian
40
g
Cambrian
Birds/Reptiles
f
Mammals/
Reptiles
Mammals
abcde
Ordovician
Cretaceous
200
180
160
120
100
Corrected amino acid changes per 100 residues
Rates of
macromolecular
evolution
Pliocene
Miocene
Oligocene
Eocene
220
j
10
6
5
800
7
8
9
Evolution of
the globins
80
6
0
1
4
3
20
2
Separation of ancestors
of plants and animals
0
900 1000 1100 1200 1300 1400
Millions of years since divergence
After Dickerson (1971)
Homology
• Orthologs
– Divergence (sequence change) follows speciation
– Similarity can be used to construct phylogeny
– Multiple orthologs can be present
• Paralogs
– Divergence follows duplication
• Xenologs
– Horizontal interspecies transfer of genes
• Homoplasy (similarity not due to common ancestry)
– Parallelism
– Convergence
– Reversal
Orthologs and paralogs
Homology vs. Homoplasy
X
X
Homology: similar traits
inherited from a common
ancestor
X
X
Homoplasy: similar traits are
not directly caused by common
ancestry (convergent
evolution).
Unique and unreversed characters
- Hair
• Because hair evolved only once and is
unreversed it is homologous and provides
unambiguous evidence for the clade Mammalia
Human
Lizard
HAIR
Frog
change
or step
Dog
absent
present
Homoplasy - independent evolution
- Tails
• Loss of tails evolved independently in
humans and frogs - there are two steps on
the true tree
Lizard
Human
TAIL
Frog
Dog
absent
prese
nt
Homoplasy - misleading evidence of
phylogeny
• If misinterpreted as homology, the absence of
tails would be evidence for a wrong tree
grouping humans with frogs and lizards with dogs
Human
Lizard
TAIL
Frog
Dog
absent
present
Homology: limb structure
Homoplasy: wings
Homoplasy in molecular data
• Incongruence and therefore homoplasy can be common in
molecular sequence data
• One reason is that characters have a limited number of
alternative character states ( e.g. A, G, C and T)
• In addition, these states are chemically identical so that
homology and homoplasy are equally similar and cannot
be distinguished through detailed study of structure or
development
Types of substitution
A
C
A
A
T
C
C
A
T
C
G
A
C
G
A
C
A
A
A
Single
1 change, 1 difference
Multiple
2 changes, 1 difference
Coincidental
2 changes, 1 difference
C
C
A
C
A
C
T
C
T
A
T
C
A
T
A
A
A
C
C
A
A
A
A
Parallel
2 changes, no difference
Convergent
3 changes, no difference
Back
2 changes, no difference
Homoplasy - reversal
• Reversals are evolutionary changes back to an
ancestral condition
• As with any homoplasy, reversals can provide
misleading evidence of relationships
True tree
Wrong tree
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9 10