Download The Neutral Theory Polymorphism

Dr. Walter Salzburger
The Neutral Theory
Polymorphism
[Greek: poly=many, morph=form]
images: www.wikipedia.com, www.clcbio.com, www.telmeds.org
The Neutral Theory | 2
The Neutral Theory | 3
Polymorphism
! ...can be defined as the existence of two or more forms
within the same population (or the same species)
! the persistence of polymorphism within a species (just as
evolutionary change between species) can be explained by:
! natural selection
! drift
The Neutral Theory | 4
Genetic Drift
! random changes in gene frequencies in a population
computer simulation of the Wright-Fisher model of random genetic drift (from: Hartl, 1997)
The Neutral Theory | 5
The Neutral Theory
! The Neutral Theory of Molecular Evolution was
formalized in the 1960s by M. Kimura
! The Neutral Theory deals with the relative
importance of natural selection and random
drift in molecular evolution
Motoo K
imura
(1924-1
994)
! The Neutral Theory became - in modifications - a
null model of molecular evolution
The Neutral Theory | 6
The Neutral Theory
! ...states that the majority of molecular evolution is driven by
neutral drift (which does not mean that the majority of
mutations are neutral!)
! Natural selection is needed to explain adaptation. Yet,
evolution at the DNA level is - according to the “neutralists”
- primarily non-adaptive
! opposite view: molecular evolution is driven by natural
selection
The Neutral Theory | 7
selectionist
neutralist
frequency of
mutations
-
0
pan-neutralist
frequency of
mutations
+
-
0
frequency of
mutations
+
-
0
+
selection coefficient
selection coefficient of a mutation:
+ mutation increases in frequency
- mutation is eliminated
0 gene frequencies drift
The Neutral Theory | 8
The Neutral Theory: evidence
! The rate of molecular evolution and the degree of
polymorphism is too high to by explained by natural
selection
! The constancy of molecular evolution (“molecular clock”)
seems to be inconsistent with natural selection
! Functionally less constrained parts evolve at higher rate
(which is the opposite of what a purely selectionist’s view
would predict)
The Neutral Theory | 9
Species
Number of loci
P(%)
H(%)
Phlox cuspicata
16
11
1,2
Limulus polypemus
25
25
5,7
28-42
18
3,8
Gryllus bimaculatus
25
58
6,3
Drosophila robusta
40
39
11
Bombus americanorum
12
0
0
Bufo americanus
14
26
11,7
Homo sapiens
71
28
6,7
Homarus americanus
Nevo (1988)
The Neutral Theory: evidence
Variation measured as percentage of polymorphic loci (P) and average heterozygosity
per individual (H)
The Neutral Theory | 10
The Neutral Theory: evidence
human/
kangaroo
rabbit/
rodent
75
llama/
cow
horse/
donkey
goat/
cow
50
25
sheep/
cow
0
0
dog/
cow
25
pig/
cow
human/
cow
human/
rodent
horse/
cow
50
75
Millions of years ago
100
125
Kimura (1993)
Nucleotide substitutions
100
The Neutral Theory | 11
The Neutral Theory: problems
! Levels of heterozygosity are too constant between different
species
! The molecular clock is not constant enough, and there are
genes not following a clock-like behavior
! Genetic variation and evolutionary rates are not always
related as predicted
The Neutral Theory | 12
The Nearly Neutral Theory!
! ...is a modified version of the “purely” neutral theory (developed
by Ohta in the 1990s)
! ...allows “nearly” neutral mutations such as slightly
disadvantageous mutations. These behave neutrally in
small populations but not in large ones (this is why genetic
variation in large populations is somewhat smaller than
predicted by the neutral theory)
! ...can in principle account of what is known about
molecular evolution
The Neutral Theory | 13
DNA sequence evolution
non-coding segment (control region)
T. moorii
N. brichardi
O. tanganicae!
ATGAATGGTGATAAGATATTGATA
ATGAGTGATAATGGAATAT-AATA
ATGAATGATATTAAGATATTGATA
----*--*-**-***----**---
protein coding segment (ND2 gene)
T. moorii
N. brichardi
O. tanganicae!
ATTCTACTCTCCCTAGGAGGCCTC
ATTCTCCTCTCACTGGGGGGCCTC
ATTCTCCTTTCACTGGGAGGCCTC
-----*--*--*--*--*------
The Neutral Theory | 14
DNA sequence evolution
The Neutral Theory | 15
DNA sequence evolution
non-synonymous substitution
...CCGCTCGTCAGCTAG...
original DNA sequence
Gly Glu Gln Ser Ile
...CCGCTCGTCAACTAG...
Gly Glu Gln Leu Ile
...CCGCTTGTCAACTAG...
Gly Glu Gln Leu Ile
synonymous substitution
The Neutral Theory | 16
dN/dS ratio
! dN/dS (Ka/Ks) provides information about the form of
sequence evolution in a gene*:
! dN/dS < 1: purifying selection (non-synonymous sites are
evolving slower than synonymous sites)
! dN/dS = 1: neutrality (non-synonymous and synonymous
sites are evolving at equal rates)
! dN/dS > 1: positive selection (non-synonymous sites are
evolving faster than synonymous sites; natural selection
has acted to change the amino acid sequence)
*dS is used as proxy for the neutral rate of molecular evolution
The Neutral Theory | 17
Zhang et al. (2002)
Pancreatic ribonuclease in colobine monkeys
douc langur
The Neutral Theory | 18
Pancreatic ribonuclease in colobine monkeys
Ka = 0.0310
substitutions per non-synonymous sites
Ks = 0.0077
substitutions per synonymous sites
(and non-coding sites)
Ka/Ks = 4.026
douc langur
The Neutral Theory | 19
Zhang et al. (2002)
Pancreatic ribonuclease in colobine monkeys
douc langur
adaptation to different pH in the colobine small intestine
The Neutral Theory | 20
Pancreatic ribonuclease in leaf-eating monkeys
douc langur
Prud’homme & Carroll (2006)
guereza
The Neutral Theory | 21
Pancreatic ribonuclease in leaf-eating monkeys
douc langur
Zhang (2006)
guereza
The Neutral Theory | 22
Tests for positive selection
! HKA test (Hudson, Kreitman and Aguade 1987):
! compares the level of polymorphism in two nuclear
loci to test for neutral versus adaptive sequence
evolution
! McDonald-Kreitman (1991) test:
! uses fixed and polymorphic sites to test for neutral
versus adaptive sequence evolution
The Neutral Theory | 23
Tests for positive selection: McDonald-Kreitman
species A
Ind.
Ind.
Ind.
Ind.
1
2
3
4
species B
ATGACTTGAT
ATGACTTRAT
ATGACTTAAT
ATGACTTAAT
fixed site
Ind.
Ind.
Ind.
Ind.
1
2
3
4
ACGACTTGAT
ACGACTTAAC
ACGACTTGAT
ACGACTTGAY
polymorphic site
The Neutral Theory | 24
Tests for positive selection: McDonald-Kreitman
Alcohol dehydrogenase gene (adh) in Drosophila
D. melanogaster (12)
D. simulans (6)
D. yakuba (24)
The Neutral Theory | 25
Tests for positive selection: McDonald-Kreitman
Differences
Fixed
sites
Polymorphic sites
Total
synonymous
SF = 17
SP = 42
SF + SP = 59
non-synonymous
NF = 7
NP = 2
NF + NP = 9
SF + NF = 24
SP + NP = 44
68
Sum
McDonald & Kreitman (1991)
The Neutral Theory | 26
Tests for positive selection: McDonald-Kreitman
NF/SF = 7/17 = 0.41
fixed non-synonymous/fixed synonymous sites
NP/SP = 2/42 = 0.048
polymorphic non-synonymous/polymorphic synonymous sites
NF/SF is significantly higher than NP/SP
Fisher’s exact test: P = 0.006
McDonald & Kreitman (1991)
The Neutral Theory | 27
Sliding Window Analysis
! Why?
! sequence evolution might not be the same over the
entire locus
sequence
dN/dS
3
2
1
0
0
sequence length
The Neutral Theory | 28
Sliding Window Analysis
Demma et al. (2006)
SIV envelope (env) protein
The Neutral Theory | 29
Testing Neutral Evolution: Tajima’s D
S... number of segregating sites
is the amount of polymorphic nucleotide sites
in the dataset
!... average pairwise difference
is the average of all pairwise differences in
the dataset
The Neutral Theory | 30
Testing Neutral Evolution: Tajima’s D
segregating sites and average pairwise differences
TaxonA
TaxonB
ATGGCAGTCT
ACGGCAGTCT
S=1
! = 0.1
The Neutral Theory | 30
Testing Neutral Evolution: Tajima’s D
segregating sites and average pairwise differences
TaxonA
TaxonB
TaxonC
ATGGCAGTCT
ACGGCAGTCT
ATGGCAGTTT
S=2
! = 0.13
The Neutral Theory | 30
Testing Neutral Evolution: Tajima’s D
segregating sites and average pairwise differences
TaxonA
TaxonB
TaxonC
TaxonD
ATGGCAGTCT
ACGGCAGTCT
ATGGCAGTTT
ATGGCGGTCT
S=3
! = 0.15
The Neutral Theory | 31
Testing Neutral Evolution: Tajima’s D
mutation rate
" = 4N#
genetic variation
(theta)
effective
population size
...can be estimated using the proportion of segregating sites or
the average pairwise differences
The Neutral Theory | 32
Testing Neutral Evolution: Tajima’s D
theta estimated from
segregating sites
D = " (!) - " (S)
theta estimated from
average genetic diversity
The Neutral Theory | 33
Testing Neutral Evolution: Tajima’s D
bottleneck,
“selective sweep”
neutral
evolution
D<0
balancing selection,
sub-division
D"0
D>0
The Neutral Theory | 34
Selective sweep & genetic hitch-hiking
beneficial mutation
“hitch-hikers”
S1
!1
S1 > S 2
!1 >>> !2
S2
!2
The Neutral Theory | 35
nucleotide diversity (!)
Selective sweep & genetic hitch-hiking
distance (kb)
beneficial allele